MedWorm provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest medical blog items that have been tagged with 'bioinformatics'. Sat, 03 Sep 2011 01:52:45 +0100 http://www.medworm.com/index.php?rid=5159569&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F08%2F23%2Fpopular-topics-at-the-biostar-qa-site%2F Conclusions? XML, ggplot2 and wordcloud are all great packages. And whilst so-called “next-generation-sequencing” might be all the rage, it’s good to see the old stalwarts of bioinformatics hanging in there: BLAST, alignment, phylogenetics, Python and Perl. It will be interesting to see how tags change over time. Filed under: bioinformatics, R, statistics, web resources Tagged: biostar, stackexchange (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=5159569 Tue, 23 Aug 2011 06:54:14 +0100 5159569 http://www.medworm.com/index.php?rid=5096848&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F08%2F05%2Fbioruby-development-feedback-on-using-git%2F Everyone likes constructive feedback. I received a couple of great comments on my previous post, which warrant a brief discussion. @vlandham points out that when the main BioRuby repository updates, you’ll want to update your local repository. Using git, you do that by adding a remote which points to the original repository, from which you can fetch updates and merge with your local version: git remote add upstream https://github.com/bioruby/bioruby.git # fetch/merge only when main repo updates git fetch upstream git merge upstream master This is described at the GitHub help page Fork A Repo. Michael points to an article titled A successful Git branching model. It suggests that when developing new features you create a feature branch (also called topic branch). This can help with t... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=5096848 Fri, 05 Aug 2011 03:15:57 +0100 5096848 http://www.medworm.com/index.php?rid=5096849&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F08%2F04%2Fa-beginners-guide-to-bioruby-development%2F I’m the “biologist-turned-programmer” type of bioinformatician which makes me a hacker, not a developer. Most of the day-to-day coding that I do goes something like this: Colleague: Hey Neil, can you write me a script to read data from file X, do Y to it and output a table in file Z? Me: Sure… (clickety-click, hackety-hack…) …there you go. Colleague: Great! Thanks. I’m a big fan of the Bio* projects and have used them for many years, beginning with Bioperl and more recently, BioRuby. And I’ve always wanted to contribute some code to them, but have never got around to doing so. This week, two thoughts popped into my head: How hard can it be? There isn’t much introductory documentation for would-be Bio* developers The answer to the firs... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=5096849 Thu, 04 Aug 2011 13:31:35 +0100 5096849 http://www.medworm.com/index.php?rid=5086448&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F08%2F01%2Fismb-coverage-on-twitter-its-possible-there-was%2F Peter writes: I wonder if part of the drop off is live bloggers moving to platforms like Twitter? I can tell you it seemed like there were almost as many tweets for one SIG (#bosc2011) as for the whole of #ISMB / #ECCB2011, and I personally didn’t post anything to FriendFeed but posted lots on Twitter. Well, there’s a problem with using Twitter for analysis of conference coverage. Let’s try searching for ISMB-related tweets using the twitteR package: library(twitteR) ismb <- searchTwitter("ismb", 1000) length(ismb) # [1] 30 If we can't archive, how can anyone else?30? Are we using twitteR properly? Running the same search at the Twitter website gives roughly the same results, plus this unhelpful message. I like Twitter – as a real-time communicatio... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=5086448 Mon, 01 Aug 2011 04:38:17 +0100 5086448 http://www.medworm.com/index.php?rid=5077940&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F07%2F28%2Fi-cant-resist-a-word-cloud-now-using-r%2F Top 1000 words in FriendFeed comments, ISMB 2008-2011The wordcloud package is word clouds for R with a difference: they look great. Of course, having just analysed online coverage of the ISMB conference, I had to run all 6 906 comments from the 2008-2011 meetings through some code. If you followed along via the Sweave code, I went as far as generating the data frame of comments, ismb.comments, then pulled the comment text into a new data frame using: data.frame(ismb.comments$body) It was then simply a case of following along with the excellent example code from the post Word Cloud in R, over at One R Tip A Day, limiting myself to the 1000 most-used words. Watch out, the TermDocumentMatrix() function from the tm package uses quite a lot of memory. Result shown at right: click image for full... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=5077940 Thu, 28 Jul 2011 10:11:36 +0100 5077940 http://www.medworm.com/index.php?rid=5077941&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F07%2F28%2Fanalysis-of-ismb-coverage-at-friendfeed-2008-2011%2F ISMB/ECCB 2011 was held between July 15-19 this year and as in previous years, FriendFeed was used to cover the meeting. Last year, I wrote a post about how to use R to analyse the coverage. I was planning something similar for 2011 when I thought: we have 4 years of ISMB at FriendFeed now – why not look at all of them? So I did. Read on for the details. 1. First – an apology In my post from last year, I included some R code which will grab a FriendFeed feed in JSON format using the API and convert it to an R list. I would have used it again this year, except that the ISMB 2008 feed is no longer a complete archive of the 2008 meeting. This is, unfortunately, my fault – but all is not lost. I decided to leave FriendFeed earlier this year and began by deleting the se... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=5077941 Thu, 28 Jul 2011 02:40:17 +0100 5077941 http://www.medworm.com/index.php?rid=4841830&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F05%2F18%2Fhow-to-create-a-partial-ucsc-genome-mysql-database%2F File under: simple, but a useful reminder UCSC Genome Bioinformatics is one of the go-to locations for genomic data. They are also kind enough to provide access to their MySQL database server: mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A However, users are given fair warning to “avoid excessive or heavy queries that may impact the server performance.” It’s not clear what constitutes excessive or heavy but if you’re in any doubt, it’s easy to create your own databases locally. It’s also easy to create only the tables that you require, as and when you need them. As an example, here’s how you could create only the ensGene table for the latest hg19 database. Here, USER and PASSWD represent a local MySQL user and password with full privileg... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4841830 Wed, 18 May 2011 04:54:10 +0100 4841830 http://www.medworm.com/index.php?rid=4734450&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F04%2F21%2Flists-of-urls-are-so-1990s%2F Subtitle: “Why some projects are not worth your valuable time and skills.” Let’s wrap up this exploration of how to extract URLs associated with NAR Database articles. I’m tempted to start with the summary: don’t bother – just Google it. If you want that, skip to the end. First: forget PubMed. This query: "Nucleic Acids Res"[JOUR] "Database issue"[ISS] is all well and good except that between 1998 and 2004, the NAR Database Issue was not named “Database issue”; it just has a volume number, like the other issues. If you insist on trying to extract URLs from PubMed abstracts, be prepared for frustration. They include every valid variant imaginable (with/without a leading “http://”) and many invalid variants (b... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4734450 Wed, 20 Apr 2011 14:08:18 +0100 4734450 http://www.medworm.com/index.php?rid=4734452&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F04%2F19%2Fwhy-cant-pubmed-or-academic-journals-get-the-basics-right%2F A recent question at BioStar asked “Is the NAR database list available in a computer readable format?” The short answer is “no” and Pierre has done some excellent preliminary work to address the issue. I’ve been working on a database and web application to check the associated URLs but quite frankly, this is tedious, a waste of everyone’s time and could be entirely avoided if the publishing industry did a better job. All that’s required is that either NAR or PubMed provide structured data – XML, Medline format, I don’t care what – containing a field that looks something like this: URL http://a.valid.url.goes.here That way, we could all avoid writing regular expressions to detect URLs in abstracts. No wait – to detect brok... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4734452 Tue, 19 Apr 2011 04:45:29 +0100 4734452 http://www.medworm.com/index.php?rid=4676317&cid=t_104194_139_f&fid=38879&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FVirologyBlog%2F%7E3%2FYgb2d_p5qu4%2F This week’s addition to the virology toolbox was written by Chris Upton Sequence Searcher is a Java program that allows users to search for specific sequence motifs in protein or DNA sequences. For example, it can be used to identify restriction enzyme cleavage sites or find similar sequence patterns among multiple sequences. Most searches run in a few seconds. Sequence Searcher is part of the Virology.ca suite of programs available at the University of Victoria. Help files: Quick start How-to Some of the key features of Sequence Searcher include: Searching through multiple sequences Use of regular expressions or fuzzy search patterns. Searching for patterns on both strands of a DNA sequence Graphical representation of results and ability to save search results It can run on multiple ... virology blog blogs http://www.medworm.com/rss/comments.php?id=4676317 Mon, 04 Apr 2011 19:14:42 +0100 4676317 http://www.medworm.com/index.php?rid=4622439&cid=t_104194_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FnTu2PhfwR7w%2F Here’s a few courses to consider for the summer that cover informatics, genomics, and metagenomics analysis focusing on next generation sequencing. The deadlines are fast approaching so apply soon. (There are undoubtably more, and I’m happy to post here if you have suggestions) Workshop on Comparative Genomics Course dates: 10 – 23 July 2011 The Workshop on Comparative Genomics consists of a series of lectures, demonstrations and computer laboratories that cover various aspects of comparative genomics. Faculty are chosen exclusively for their effectiveness in teaching theory and practice in comparative genomics. Included among the faculty are developers and other experts in the use of computer programs and packages such as Ensembl and Galaxy who provide demonstrations a... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=4622439 Mon, 21 Mar 2011 22:40:20 +0100 4622439 http://www.medworm.com/index.php?rid=4527937&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F02%2F28%2Fnature-on-reproducible-research%2F I imagine that most people, when asked “do you think that independent confirmation of research findings is important?” would answer “yes”. I also imagine, when told that in most cases this is not possible, that those people might be concerned or perhaps incredulous. However, this really is the case, which is why I spend much of my working life in a state of concern and incredulity. Over the years, many articles have been written on how to improve this state of affairs by adopting best practices, collectively-termed reproducible research. One of the latest is an editorial in Nature. I’ve pulled out a few quotes for discussion. To ensure their results are reproducible, analysts should show their workings These words form the article summary. Absolutely. No argu... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4527937 Mon, 28 Feb 2011 11:46:59 +0100 4527937 http://www.medworm.com/index.php?rid=4482924&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F02%2F16%2Freal-bioinformaticians-write-code%2F A lot of questions at BioStar begin along these lines: Where can I find…? I am looking for a resource…? Is there some database…? I tweeted some concerns about this: Many #biostar questions begin “I am looking for a resource..”. The answer is often that you need to code a solution using the data you have. Chris tweeted back: @neilfws Lit. or Google search is first step, asking around is the next logical step. (Re-)inventing wheels is last. Worth asking, IMHO. We had a little chat and I realised that 140 characters or less was not getting my point across (not for the first time). What I was trying to say was something like this. Chris is quite right; searching, then asking for existing solutions is the correct first approach. However, the tone of certain ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4482924 Wed, 16 Feb 2011 12:30:47 +0100 4482924 http://www.medworm.com/index.php?rid=4473053&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F02%2F14%2Fgetting-stuff-into-mongodb%2F One of the aspects I like most about MongoDB is the “store first, ask questions later” approach. No need to worry about table design, column types or constant migrations as design changes. Provided that your data are in some kind of hash-like structure, you just drop them in. Ruby is particularly useful for this task, since it has many gems which can parse common formats into a hash. Here are 3 quick examples with relevance to bioinformatics. 1. JSON JSON is a good fit for MongoDB; when you view a document (represented internally as BSON), the structure looks just the same as the original JSON. I use json/pure as in this example, which grabs expression data for a gene from the Gene Expression Atlas API: require 'open-uri' require 'json/pure' require 'mongo' db = Mongo::Conn... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4473053 Mon, 14 Feb 2011 06:52:41 +0100 4473053 http://www.medworm.com/index.php?rid=4460107&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FptsXAmMBwxg%2F I love Bioconductor, I really do. It’s a great framework, nice set of tools that do anything that you want (not that I would want to do phylogeny with it, topic for another post). But as anything scientific it has its drawbacks, and I can point three of them: 1 – Installing packages – we’re having problems running one package, what requires us to modify R’s compilation parameters from time to time, uninstall and reinstall things. And the most annoying thing is when you have a fresh R binary and framework, you do a basic install first and when you want another package installed if it has dependencies that are already in the system, they are downloaded and installed again. 2 – Website – Looking from the design and navigation point of view, it’... Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=4460107 Fri, 11 Feb 2011 01:59:05 +0100 4460107 http://www.medworm.com/index.php?rid=4455409&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F02%2F10%2Fconservative-with-a-small-c-research%2F This is really interesting. I’m reading it at work so I can’t tell you if it’s behind the paywall, but I sincerely hope not; it deserves to be read widely: Edwards, A.M. et al. (2011) Too many roads not taken. Nature 470: 163–165 doi:10.1038/470163a Most protein research focuses on those known before the human genome was mapped. Work on the slew discovered since, urge Aled M. Edwards and his colleagues. The article includes some nicely-done bibliometric analysis. I’ve lifted a few quotes that illustrate some of the key points. More than 75% of protein research still focuses on the 10% of proteins that were known before the genome was mapped Around 65% of the 20,000 kinase papers published in 2009 focused on the 50 proteins that were the ‘hottest’ in... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4455409 Thu, 10 Feb 2011 02:02:48 +0100 4455409 http://www.medworm.com/index.php?rid=4455411&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FMjH3ejV23XU%2F This was asked by Neil, and I think I can answer it. Clearly, the publication is way more important than the actual product, sadly so. The paper (or letter, comment, correspondence, whatever it is) that he points out is a complete joke, the website is a complete joke, as the most complete page on it is the CV of each member in the project. It seems that in this case there’s no peer review involved, but I bet the “authors” will dutifully used the reference in their CV. I can say from experience that even with peer review, the actual product is irrelevant, at least in some of the cases. Sometimes software that I published were completely dissected by the reviewers and it was clear that they installed the application and tested. In other cases, usually the rejected ones, the... Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=4455411 Wed, 09 Feb 2011 16:55:16 +0100 4455411 http://www.medworm.com/index.php?rid=4455410&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F02%2F09%2Falgorithms-running-day-and-night%2F Warning: contains murky, somewhat unstructured thoughts on large-scale biological data analysis Picture this. It’s based on a true story: names and details altered. Alice, a biomedical researcher, performs an experiment to determine how gene expression in cells from a particular tissue is altered when the cells are exposed to an organic compound, substance Y. She collates a list of the most differentially-expressed genes and notes, in passing, that the expression of Gene X is much lower in the presence of substance Y. Bob, a bioinformatician in the same organisation but in a different city to Alice, is analysing a public dataset. This experiment looks at gene expression in the same tissue but under different conditions: normal compared with a disease state, Z Syndrome. He also notes ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4455410 Wed, 09 Feb 2011 03:41:21 +0100 4455410 http://www.medworm.com/index.php?rid=4450454&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F02%2F08%2F2462%2F The Nature stable of journals. A byword for quality, integrity, impact. Witness this recent offering from Nature Biotechnology: Bale, S. et al. (2011) MutaDATABASE: a centralized and standardized DNA variation database. Nature Biotechnology 29, 117–118 doi:10.1038/nbt.1772 Unfortunately, although it describes an open, public database, the article itself costs $32 to read without subscription (update: it’s freely available as of one day after this post). Not to be deterred, I went to investigate MutaDATABASE itself. The alarm bells began to ring right there on the index page (see screenshot, right). Could that be right? I tried several browsers, in case of a rendering problem. Same result – no contents. There seems to be something missing Clicking on some of the link... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4450454 Tue, 08 Feb 2011 13:10:50 +0100 4450454 http://www.medworm.com/index.php?rid=4405961&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F01%2F27%2Fapis-have-let-me-down-part-12-arrayexpress%2F The API – Application Programming Interface – is, in principle, a wonderful thing. You make a request to a server using a URL and back come lovely, structured data, ready to parse and analyse. We’ve begun to demand that all online data sources offer an API and lament the fact that so few online biological databases do so. Better though, to have no API at all than one which is poorly implemented and leads to frustration? I’m beginning to think so, after recent experiences on both a work project and one of my “fun side projects”. Let’s start with the work project, an attempt to mine a subset of the ArrayExpress microarray database. 1. Introduction ArrayExpress is an online database of microarray experiments, organised by both gene (the expression at... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4405961 Thu, 27 Jan 2011 09:04:11 +0100 4405961 http://www.medworm.com/index.php?rid=4394664&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2Fz93LQqVL8yM%2F 1 – Good Omens: The Nice and Accurate Prophecies of Agnes Nutter, Witch 2 – The Cobra (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=4394664 Mon, 24 Jan 2011 15:24:31 +0100 4394664 http://www.medworm.com/index.php?rid=4355845&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FlpUl5_FYuYs%2F $1,000 reward offered for stolen cancer research laptop: Medical researchers in Oklahoma are offering a no-questions-asked $1,000 reward for the return of a stolen laptop that contains years of research on prostate cancer. Sook Shin lost the 13-inch white MacBook last Sunday after thieves smashed the window of the car she shares with husband, Ralf Jankecht, and made off with the laptop. Data on the machine was not backed up. So, you never backup your data or have an extra copy, and, at the same time, value “years” of research just one thousand dollars. Pathetic. (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=4355845 Sun, 16 Jan 2011 22:03:59 +0100 4355845 http://www.medworm.com/index.php?rid=4331166&cid=t_104194_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2011%2F01%2F11%2Fopenpcr-%25e2%2580%2593-open-source-hackable-pcr-machine%2F I’ve recently come across an exciting project, OpenPCR that aims to build a PCR machine by using simple elements that you can buy anywhere. You can pre-order the machine for 512$. We want to produce an open design for a PCR machine. Our goal is to start this project up quickly and get a working prototype made for Maker Faire. After that, add on applications such as SNPs or PCR kits or synthetic biology. A DIY Xerox machine for DNA: A fast, computer controlled PCR machine that uses normal PCR tubes and may be built mostly with off the shelf components + free schematics. It does thermal cycling as well as boil, cool, and freeze (4C) samples. Please help them! You watch a presentation about the project here. (Source: ScienceRoll) ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=4331166 Tue, 11 Jan 2011 04:04:01 +0100 4331166 http://www.medworm.com/index.php?rid=4326923&cid=t_104194_107_f&fid=35041&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fscienceblogs%2Fdigitalbio%2F%7E3%2FfXTtj3bqUnQ%2Fnext_gene_sequencing_results_a.php I had the good fortune on Thursday to hear a fascinating talk on deep transcriptome analysis by Chris Mason, Assistant Professor, at the Institute for Computational Biomedicine at Cornell University.  Several intriguing observations were presented during the talk.  I'll present the key points first and then discuss the data.These data concern the human transcriptome, and at least some of the results are supported by  follow on studies with data from the pigmy tailed macaque.Some of the most interesting points from Mason's talk were: A large fraction of the existing genome annotation is wrong.We have far more than 30,000 genes, perhaps as many as 88,000.  About ten thousand genes use over 6 different sites for polyadenylation.98% of all genes are alternatively spliced.S... Discovering Biology in a Digital World blogs http://www.medworm.com/rss/comments.php?id=4326923 Sat, 08 Jan 2011 23:36:32 +0100 4326923 http://www.medworm.com/index.php?rid=4285301&cid=t_104194_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FrYtx4OOtgDY%2F Though a bit cliche, I think the metaphor of “presents under the tree” of some new plant pathogen genomes summarized in 4 recent publications is still too good to resist.  There are 4 papers in this week’s Science that will certainly make a collection of plant pathogen biologists very happy. There are also treats for the general purpose genome biologists with descriptions of next generation/2nd generation sequencing technologies, assembly methods, and comparative genomics. Much more inside these papers than I am summarizing so I urge you to take look if you have access to these pay-for-view articles or contact the authors for reprints to get a copy. These include the genome of biotrophic oomycete and Arabidopsis pathogen Hyaloperonospora arabidopsidis (Baxter et al). Wh... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=4285301 Thu, 23 Dec 2010 16:11:50 +0100 4285301 http://www.medworm.com/index.php?rid=4266103&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2F2ODyTDMXJP4%2F 1 – The New New Thing: A Silicon Valley Story 2 – What Do You Care What Other People Think?: Further Adventures of a Curious Character 3 – Days Between Stations: A Novel 4 – A Bridge Too Far: The Classic History of the Greatest Battle of World War II 5 – The Man Who Smiled: A Kurt Wallander Mystery (4) (Vintage Crime/Black Lizard) 6 – Silence of the Grave (Reykjavik Murder Mysteries, No. 2) 7 – What Mad Pursuit: A Personal View of Scientific Discovery 8 – Seed of Light 9 – American Psycho 10 – Glamorama (Vintage Contemporaries) 11 – Eats, Shoots & Leaves: The Zero Tolerance Approach to Punctuation 12 – Slaughterhouse-Five: A Novel 13 – Bellini e os Espíritos 14 – Drop the Dead Donkey (A Channel Four B... Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=4266103 Thu, 16 Dec 2010 13:47:49 +0100 4266103 http://www.medworm.com/index.php?rid=4259104&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2F6H__2l2LHQk%2F - Movie: Inception, not the best one, but highly entertaining, worst: none - Book: The Big Short: Inside the Doomsday Machine, worst Days Between Stations: A Novel - Website: Kissing Suzy Kolber, worst: Mendeley - Software: Things, worst Mendeley, by 1000 miles - TV: best Walking Dead and Modern Family worst: any TLC show - Purchase: snow tyres, again - Money-grabbing-scheme: Global Warming or Climate Change, again - Politician: no best in the category, but the worst is the Brazilian President. - Music: most of the things I listened to were great, but the new Superchunk takes the cake - Best programming language was still Python, worst, still Java - Best operating system was Snow Leopard, worst, any Windows (including XP) (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=4259104 Tue, 14 Dec 2010 00:32:03 +0100 4259104 http://www.medworm.com/index.php?rid=4241892&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FR9BLDY2s-UE%2F (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=4241892 Wed, 08 Dec 2010 14:58:28 +0100 4241892 http://www.medworm.com/index.php?rid=4233342&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FUYf3PeNzAjs%2F Tyring to download a file from Microsoft.com on Internet Explorer 8, under Windows 2008 server. (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=4233342 Mon, 06 Dec 2010 18:36:12 +0100 4233342 http://www.medworm.com/index.php?rid=4225533&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2F9UIV_ik5mBs%2F I have received several emails about my coveted Best and Words of 2010. So, to placate the hordes and get some email relief, here is a short list of the worst of 2010: Worst software: Mendeley More next week, or the following. (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=4225533 Thu, 02 Dec 2010 22:00:00 +0100 4225533 http://www.medworm.com/index.php?rid=4220387&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FprKwoYShGP0%2F About eight months ago I started using Biostar as I saw it as a great opportunity to exchange some ideas, concepts, tips in biology and bioinformatics. I even mentioned the website in this space, trying to bring more people to the mix; at the time the community wasn’t big enough, and some days went by without any question being posted. But a couple of months ago my interest started to go down the drain. I don’t know if it was the constant next-generation sequencing barrage of questions every day, if it was the infantile blog/twitter posts from members competing for points or maybe the lack of votes for some answers that I posted (that’s selfish on my part, I admit). But at some point it seemed that the website turned into a competition of CVs or knowledge, very different ... Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=4220387 Wed, 01 Dec 2010 15:44:44 +0100 4220387 http://www.medworm.com/index.php?rid=4159400&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FlVt_gVFEPzQ%2F In Flanders Fields Lieutenant Colonel John McCrae Canadian Army In Flanders Fields the poppies blow Between the crosses row on row, That mark our place; and in the sky The larks, still bravely singing, fly Scarce heard amid the guns below. We are the Dead. Short days ago We lived, felt dawn, saw sunset glow, Loved and were loved, and now we lie In Flanders fields. Take up our quarrel with the foe: To you from failing hands we throw The torch; be yours to hold it high. If ye break faith with us who die We shall not sleep, though poppies grow In Flanders fields. (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=4159400 Thu, 11 Nov 2010 15:02:16 +0100 4159400 http://www.medworm.com/index.php?rid=4152098&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F11%2F09%2Fhow-open-source-and-biostar-saved-a-project%2F This is the story of how an open source project and a science communication tool combined to save the day. 1. November 2nd 2010 I receive an email from colleagues at my previous workplace. They are trying to publish some proteomics data and the journal has stipulated that raw data and “annotated peptide mass fingerprint spectra” must be made available. The data that they have come from a machine called a Voyager-DE STR MALDI-TOF mass spectrometer. They are binary files with the suffix “.dat”. No-one is quite sure what to do with them. To plot the spectra we need a file that contains, as a minimum, the intensity and m/z ratio for each peak. Oh, that we had simple CSV files, or at least something in plain ASCII text. 2. November 5th 2010 I get to work. Some web searc... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4152098 Tue, 09 Nov 2010 13:15:22 +0100 4152098 http://www.medworm.com/index.php?rid=4142921&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F11%2F08%2Ffirst-publication-for-a-while-a-review-of-nuclear-localization%2F Thanks to my former colleagues at UQ for involving me with: Marfori, M., Mynott, A., Ellis, J.J., Mehdid, A.M., Saunders, N.F.W., Curmi, P.M., Forwood, J.K., Bodén, M. and Kobe, B. (2010) Molecular basis for specificity of nuclear import and prediction of nuclear localization. Biochimica et Biophysica Acta (BBA) – Molecular Cell Research: in press – uncorrected proof. A real group effort this one; I made a small contribution to Section 3 – Nuclear localization databases and computational tools to predict nuclear localization. Note that this version is an uncorrected proof and may change slightly before full publication. If nuclear localization is your thing, I think you’ll enjoy it; it’s a pretty comprehensive review. Filed under: bioinformatics, publicatio... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4142921 Mon, 08 Nov 2010 03:06:50 +0100 4142921 http://www.medworm.com/index.php?rid=4139404&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F11%2F05%2Fwhat-the-world-needs-is-lists-of-entrez-database-fields%2F You know the problem. You want to qualify your NCBI/Entrez database search term using a field. For example: “autism[TIAB]“, to search PubMed for the word autism in either Title or Abstract. Problem – you can’t find a list of fields specific to that database. Now you can. Follow the links in this public Dropbox file, to see a CSV file containing name, full name and description of the fields for each Entrez database. Code to generate the files is listed below. This may or may not be the first in an occasional, irregular “what the world needs” series. #!/usr/bin/ruby require 'rubygems' require 'bio' require 'hpricot' require 'open-uri' Bio::NCBI.default_email = "me@me.com" ncbi = Bio::NCBI::REST.new ncbi.einfo.each do |db| puts "Processin... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4139404 Fri, 05 Nov 2010 04:31:55 +0100 4139404 http://www.medworm.com/index.php?rid=4121910&cid=t_104194_107_f&fid=36584&url=http%3A%2F%2Fwww.biotech-weblog.com%2F39444424%2Ftough_fibers_from_transgenic_silkworms.php silk fibers from transgenic wormsA startup company - Kraig Biocraft Laboratories - were able to make made genetically modified silkworms that produce fibers incorporating spider-silk proteins. The product fibers are a lot stronger and flexible and finer than silk made by normal silkworms. Kraig Biocraft believes that they will be able to match the properties of spider silk within the next year and hopes to sell the first generation of fibers to companies that will make stronger everyday silk products. Their ultimate goal ... (Source: The Biotech Weblog) The Biotech Weblog blogs http://www.medworm.com/rss/comments.php?id=4121910 Sun, 31 Oct 2010 04:39:33 +0100 4121910 http://www.medworm.com/index.php?rid=4119468&cid=t_104194_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FTon_fTEQfqs%2F As part of background in preparing a grant I ended up writing a few scripts to see the distribution of fungal species with ITS data in GenBank.  The whole spreadsheet of the data is public and available here and I walk you through the data generation and summary below. ITS (Internal Transcribed Spacer) is the typically used barcode for identifying fungi at the species level as it works for most (but not all) groups of Fungi. It falls between highly conserved nuclear rDNA genes (18S, 5.8S, 28S) but tends to be hypervariable making it a reasonable locus for identification of species since it tends to be unique between species but fairly unchanged among individuals from the same species. You can see a Map of the amplified region from Tom Brun’s site or info at Rytas Vilgalys’s ... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=4119468 Fri, 29 Oct 2010 06:10:20 +0100 4119468 http://www.medworm.com/index.php?rid=4117881&cid=t_104194_139_f&fid=38879&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FVirologyBlog%2F%7E3%2Fp2NN3Sk-Aro%2F This week’s addition to the virology toolbox was written by Chris Upton (Disclaimer: BBB was developed in the Upton lab, so this is a biased review.) This will be a multi-part posting describing the key features of BBB. Base-By-Base (BBB) is a Java (platform independent) multiple sequence alignment (MSA) editor. Development was begun many years ago to provide a virologist-friendly tool to work with MSAs of proteins, gene sequences and also genome sequences (up to about 500 kb). Over the years we have added many unique features, as they have been needed by our own research with a variety of virus genomes; development has been driven by the users – who spend a lot of their day looking at a variety of MSAs! BBB is available here. The program is Open Source and freely available to all acad... virology blog blogs http://www.medworm.com/rss/comments.php?id=4117881 Tue, 26 Oct 2010 21:55:02 +0100 4117881 http://www.medworm.com/index.php?rid=4085962&cid=t_104194_139_f&fid=38879&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FVirologyBlog%2F%7E3%2FNqu0iOoEXbw%2F This week’s addition to the virology toolbox was written by Chris Upton The Jalview package: a multiple alignment editor. This software is primarily aimed at the alignment of protein sequences. Some of the key features are: It allows you to edit the alignment It has functions to display associated protein structures It can connect to software to predict protein secondary structure It’s under active development Jalview has great documentation and tutorials More: Overview, Documentation Tips: Although you can install Jalview on your computer very easily, using the Start with Java Web Start button is even easier and ensures you always have the latest version of the software. There is also an Applet version of Jalview that is intended to be an alignment viewer – it doesn’t have ... virology blog blogs http://www.medworm.com/rss/comments.php?id=4085962 Wed, 20 Oct 2010 19:19:07 +0100 4085962 http://www.medworm.com/index.php?rid=4086444&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2F3z4f7aCiYtM%2F 1 – The New New Thing: A Silicon Valley Story 2 – What Do You Care What Other People Think?: Further Adventures of a Curious Character 3 – Days Between Stations: A Novel 4 – A Bridge Too Far: The Classic History of the Greatest Battle of World War II 5 – The Man Who Smiled: A Kurt Wallander Mystery (4) (Vintage Crime/Black Lizard) 6 – Silence of the Grave (Reykjavik Murder Mysteries, No. 2) 7 – What Mad Pursuit: A Personal View of Scientific Discovery 8 – Seed of Light 9 – American Psycho 10 – Glamorama (Vintage Contemporaries) 11 – Eats, Shoots & Leaves: The Zero Tolerance Approach to Punctuation 12 – Slaughterhouse-Five: A Novel 13 – Bellini e os Espíritos 14 – Drop the Dead Donkey (A Channel Four B... Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=4086444 Wed, 20 Oct 2010 16:50:00 +0100 4086444 http://www.medworm.com/index.php?rid=4074315&cid=t_104194_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2010%2F10%2F15%2Fbioinformatics-and-web-2-0%2F The number of communities and repositories dedicated to Bioinformatics is rapidly growing so finding relevant resources takes more and more time and efforts. Webicina, as usual, selected only relevant social media resources such as GenomeWeb Bioinform news site, Science in the Open blog, Molecular Station community, Bioinformatics Tutorials Youtube channel or OpenNetWare wiki. Webicina’s new Bioinformatics and Web 2.0 collection features even more social media resources. If you also want to follow easily these selected resources in a personalized way, here is PeRSSonalized Bioinformatics, the simplest, free, customizable, multi-lingual medical information aggregator. Here is table of contents: News and Information on Bioinformatics Bioinformatics in the Blogosphere Bioinformatics... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=4074315 Fri, 15 Oct 2010 17:11:51 +0100 4074315 http://www.medworm.com/index.php?rid=4073526&cid=t_104194_139_f&fid=38879&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FVirologyBlog%2F%7E3%2FvHqbPksYzRM%2F This week’s addition to the virology toolbox was written by Chris Upton Generating multiple sequence alignments (MSA) is one of the most commonly used bioinformatics techniques. The “sequences” to be compared can be DNA (promoters, genes, genomes) or proteins. Note that the length and number of sequences to be aligned has an impact on the methods (algorithms) that can be used; what is suitable for aligning 20 proteins probably won’t work for alignment of 5 poxvirus genomes (200 kb each). Some useful links: Wikipedia: multiple sequence alignment Wikipedia: sequence alignment Wikipedia: list of sequence alignment software Protein Multiple Sequence Alignment: Book chapter by Chuong B. Do and Kazutaka Katoh Sequence alignment: Lecture notes by Per Kraulis Another list of tools So yo... virology blog blogs http://www.medworm.com/rss/comments.php?id=4073526 Fri, 15 Oct 2010 16:24:12 +0100 4073526 http://www.medworm.com/index.php?rid=4053427&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F10%2F09%2Fbiostar-users-of-the-world-unite%2F Egon writes: Can someone please plot the BioStar users on a Google Map? Sounds like a challenge. Let’s go. 1. Harvesting user IP addresses BioStar user profiles (here’s mine) include a location field. It’s free text and optional, which means that location is missing or inaccurate for many users. However, if you’re logged into BioStar (and perhaps, if you’re a moderator – I’m not sure), you’ll see a field that says: Last activity: 4 hours ago from XXX.XXX.XXX.XXX where “XXX.XXX.XXX.XXX” is either an IP address or, for your own page, the text “this IP address” (assuming your latest activity was from your current machine). IP addresses can be used for geolocation – we’ll see how shortly. The problem is th... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4053427 Sat, 09 Oct 2010 07:04:46 +0100 4053427 http://www.medworm.com/index.php?rid=4045277&cid=t_104194_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2010%2F10%2F08%2Fprogramming-dna%2F In 2007, Drew Endy (Endy Lab) talked about Programming DNA, a 2-bit language for engineering biology, at the 24th Chaos Communication Congress on biological engineering and synthetic biology. This talk will introduce current best practice in biological engineering, including an overview of how to order synthetic DNA and how to use and contribute standard biological parts to an open source collection of genetic functions. The talk will also discuss issues of human practice, including biological safety, biological security, ownership, sharing, and innovation in biotechnology, community organization, and perception across many different publics. (Hat Tip: Biopunk) (Source: ScienceRoll) ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=4045277 Fri, 08 Oct 2010 12:42:56 +0100 4045277 http://www.medworm.com/index.php?rid=4031293&cid=t_104194_107_f&fid=36584&url=http%3A%2F%2Fwww.biotech-weblog.com%2F39444424%2Faggressive_skin_cancer_gene_found.php © EmmaLeeSnowCutaneous squamous cell carcinoma (SCC) is an aggressive kind of skin cancer that usually spreads to other parts of the body. Now, according to a study published by the Arizona Cancer Center, Mayo Clinic and the Translational Genomics Research Institute (TGen), he loss of a gene known as INPP5A could predict the onset and track the progression of cutaneous squamous carcinoma. Targeting the said gene - INPP5A - will provide physicians with better ways of preventing and treating this aggressive skin cancer. ... (Source: The Biotech Weblog) The Biotech Weblog blogs http://www.medworm.com/rss/comments.php?id=4031293 Mon, 04 Oct 2010 12:06:24 +0100 4031293 http://www.medworm.com/index.php?rid=3987188&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F09%2F21%2Fnodalpoint-now-in-glorious-stereophonic-audio%2F Nodalpoint Conversations is, in Greg’s words, “Nodalpoint rebooted as a podcast”. Long-time readers will remember Nodalpoint, a bioinformatics community where many of us first came together. In the “pilot” episode, Greg and I chat (via Skype between Leiden and Sydney) about all things bioinformatics. It was a new experience for me and one which I greatly enjoyed, despite being somewhat unsettled by the sound of my own recorded voice. Check out Episode 1 of Nodalpoint Conversations. It’s as close to proof of my existence as you’ll get. Then follow nodalconv on Twitter. Filed under: bioinformatics, multimedia, nodalpoint, web resources Tagged: podcast (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3987188 Tue, 21 Sep 2010 10:15:21 +0100 3987188 http://www.medworm.com/index.php?rid=3987189&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FlKQNw7qerFY%2F 1 – The New New Thing: A Silicon Valley Story 2 – What Do You Care What Other People Think?: Further Adventures of a Curious Character 3 – Days Between Stations: A Novel 4 – A Bridge Too Far: The Classic History of the Greatest Battle of World War II 5 – The Man Who Smiled: A Kurt Wallander Mystery (4) (Vintage Crime/Black Lizard) 6 – Silence of the Grave (Reykjavik Murder Mysteries, No. 2) 7 – What Mad Pursuit: A Personal View of Scientific Discovery 8 – Seed of Light 9 – American Psycho 10 – Glamorama (Vintage Contemporaries) 11 – Eats, Shoots & Leaves: The Zero Tolerance Approach to Punctuation 12 – Slaughterhouse-Five: A Novel 13 – Bellini e os Espíritos 14 – Drop the Dead Donkey (A Channel Four B... Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=3987189 Mon, 20 Sep 2010 14:25:27 +0100 3987189 http://www.medworm.com/index.php?rid=3969040&cid=t_104194_107_f&fid=36584&url=http%3A%2F%2Fwww.biotech-weblog.com%2F50226711%2Fpreeclampsiapredicting_metabolic_markers_newly_found.php © mahalieFourteen simple metabolites that predict preeclampsia in early pregnancy with high accuracy have been detected by a team of international scientists. Marked by high blood pressure and excess protein in a pregnant woman's urine after 20 weeks of pregnancy, preeclampsia can lead to serious and even fatal complications for both the mother and the baby when left untreated. At the moment, there is no test that predicts preeclampsia and there is also no cure other than the baby's delivery. Reporting in Hypertension: ... (Source: The Biotech Weblog) The Biotech Weblog blogs http://www.medworm.com/rss/comments.php?id=3969040 Tue, 14 Sep 2010 21:50:08 +0100 3969040 http://www.medworm.com/index.php?rid=3946635&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F09%2F09%2Ftrust-no-one-errors-and-irreproducibility-in-public-data%2F Just when I was beginning to despair at the state of publicly-available microarray data, someone sent me an article which…increased my despair. The article is: Deriving chemosensitivity from cell lines: Forensic bioinformatics and reproducible research in high-throughput biology (2009) Keith A. Baggerly and Kevin R. Coombes Ann. Appl. Stat. 3(4): 1309-1334 It escaped my attention last year, in part because “Annals of Applied Statistics” is not high on my journal radar. However, other bloggers did pick it up: see posts at Reproducible Research Ideas and The Endeavour. In this article, the authors examine several papers in their words “purporting to use microarray-based signatures of drug sensitivity derived from cell lines to predict patient response.” They f... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3946635 Thu, 09 Sep 2010 04:57:34 +0100 3946635 http://www.medworm.com/index.php?rid=3946226&cid=t_104194_139_f&fid=38879&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FVirologyBlog%2F%7E3%2Fh3VFo_mP53g%2F This week’s addition to the virology toolbox was written by Danielle Coulson and Chris Upton Comparing genomes of viral strains can provide very useful insight into evolutionary relationships. Recombination, defined by Posada et al (2001) as the exchange of genetic information between two nucleotide sequences, is quite common in many viruses. Because recombination accounts for much of the genetic diversity observed between viral strains, it is of interest to decipher where the origins of recombinant sequences are, and to know which viral strains are likely to have undergone recombination. Several programs exist to detect recombination among genomes and to identify breakpoints in sequences, which represent recombinant regions. A few are described here, using HIV-1 strains isolated from Ug... virology blog blogs http://www.medworm.com/rss/comments.php?id=3946226 Wed, 08 Sep 2010 17:05:09 +0100 3946226 http://www.medworm.com/index.php?rid=3929412&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2F2ShjSh3mG9w%2F 1 – The New New Thing: A Silicon Valley Story 2 – What Do You Care What Other People Think?: Further Adventures of a Curious Character 3 – Days Between Stations: A Novel 4 – A Bridge Too Far: The Classic History of the Greatest Battle of World War II 5 – The Man Who Smiled: A Kurt Wallander Mystery (4) (Vintage Crime/Black Lizard) 6 – Silence of the Grave (Reykjavik Murder Mysteries, No. 2) 7 – What Mad Pursuit: A Personal View of Scientific Discovery 8 – Seed of Light 9 – American Psycho 10 – Glamorama (Vintage Contemporaries) 11 – Eats, Shoots & Leaves: The Zero Tolerance Approach to Punctuation 12 – Slaughterhouse-Five: A Novel 13 – Bellini e os Espíritos 14 – Drop the Dead Donkey (A Channel Four B... Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=3929412 Thu, 02 Sep 2010 13:10:01 +0100 3929412 http://www.medworm.com/index.php?rid=3915213&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F08%2F30%2Fgeo-database-curation-lagging-behind-submission%2F GSE and GDS records in GEOmetadb by date I was reading an old post that describes GEOmetadb, a downloadable database containing metadata from the GEO database. We had a brief discussion in the comments about the growth in GSE records (user-submitted) versus GDS records (curated datasets) over time. Below, some quick and dirty R code to examine the issue, using the Bioconductor GEOmetadb package and ggplot2. Left, the resulting image – click for larger version. Is the curation effort keeping up with user submissions? A little difficult to say, since GEOmetadb curation seems to have its own issues: (1) why do GDS records stop in 2008? (2) why do GDS (curated) records begin earlier than GSE (submitted) records? library(GEOmetadb) library(ggplot2) # update database if required usi... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3915213 Mon, 30 Aug 2010 08:11:16 +0100 3915213 http://www.medworm.com/index.php?rid=3899579&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F08%2F25%2Fcommunication-failure%2F That’s my life, every day, right there: Video made using xtranormal, which looks very cool. With thanks to @BioInfo and @drewconway. Filed under: bioinformatics, humour, statistics, video Tagged: youtube (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3899579 Wed, 25 Aug 2010 05:53:36 +0100 3899579 http://www.medworm.com/index.php?rid=3896038&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2F8BKGwBBC3GY%2F 1 – The New New Thing: A Silicon Valley Story 2 – What Do You Care What Other People Think?: Further Adventures of a Curious Character 3 – Days Between Stations: A Novel 4 – A Bridge Too Far: The Classic History of the Greatest Battle of World War II 5 – The Man Who Smiled: A Kurt Wallander Mystery (4) (Vintage Crime/Black Lizard) 6 – Silence of the Grave (Reykjavik Murder Mysteries, No. 2) 7 – What Mad Pursuit: A Personal View of Scientific Discovery 8 – Seed of Light 9 – American Psycho 10 – Glamorama (Vintage Contemporaries) 11 – Eats, Shoots & Leaves: The Zero Tolerance Approach to Punctuation 12 – Slaughterhouse-Five: A Novel 13 – Bellini e os Espíritos 14 – Drop the Dead Donkey (A Channel Four B... Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=3896038 Mon, 23 Aug 2010 12:58:39 +0100 3896038 http://www.medworm.com/index.php?rid=3862139&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FTYnPBOOMfqE%2F Next time I create an API to my (few) applications, include dozens of Easter Eggs, no documentation. Some has to think about the children! (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=3862139 Thu, 12 Aug 2010 19:20:10 +0100 3862139 http://www.medworm.com/index.php?rid=3946229&cid=t_104194_139_f&fid=38879&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FVirologyBlog%2F%7E3%2FXoYc4xUkfJE%2F This week’s addition to the virology toolbox was written by Chris Upton Dotplots are an extremely useful way of visualizing comparisons of small and large DNA sequences (as well as protein sequences), providing insight into the degree of similarity, deletions, insertions and direct and indirect repeats. In a dotplot, each nucleotide, or small window of nucleotides, of one sequence is compared with every nucleotide of a second sequence. Dotplots can quickly provide an overview of the relationship between sequences. The Dotter program [1] has several very useful features including the ability to save and reload dotplots, the ability to zoom into particular regions of the plot, an option to create a multi-dotplot by aligning more than two DNA (or protein) sequences and permitting users to a... virology blog blogs http://www.medworm.com/rss/comments.php?id=3946229 Wed, 11 Aug 2010 19:48:28 +0100 3946229 http://www.medworm.com/index.php?rid=3849029&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FJPsZ-M7oZyI%2F I tried to become a Mendeley University Advisor, whatever it is. It’s the old saying “I’m in the System to destroy it from within”. Understandably, I didn’t get the gig. But what surprised me is the personal touch in the their message: Thank you for your interest in becoming a Mendeley University Advisor! We have now received hundreds of applications from around the globe representing a wide range of academic disciplines. The sheer amount of applicants has been overwhelming and we’re currently filled to capacity. Over the next few months, we will further expand the Advisor program, at which point we would love to have you join us! You don’t need to do anything to follow up, we’ve added you to the waitlist and will be in touch as space becomes available.... Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=3849029 Mon, 09 Aug 2010 15:21:22 +0100 3849029 http://www.medworm.com/index.php?rid=3831512&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2F5EX4iL-pEZ0%2F 1 – The New New Thing: A Silicon Valley Story 2 – What Do You Care What Other People Think?: Further Adventures of a Curious Character 3 – Days Between Stations: A Novel 4 – A Bridge Too Far: The Classic History of the Greatest Battle of World War II 5 – The Man Who Smiled: A Kurt Wallander Mystery (4) (Vintage Crime/Black Lizard) 6 – Silence of the Grave (Reykjavik Murder Mysteries, No. 2) 7 – What Mad Pursuit: A Personal View of Scientific Discovery 8 – Seed of Light 9 – American Psycho 10 – Glamorama (Vintage Contemporaries) 11 – Eats, Shoots & Leaves: The Zero Tolerance Approach to Punctuation 12 – Slaughterhouse-Five: A Novel 13 – Bellini e os Espíritos (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=3831512 Fri, 06 Aug 2010 22:15:38 +0100 3831512 http://www.medworm.com/index.php?rid=3798733&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F07%2F29%2Flazy-post-a-life-scientists-best-of%2F When stuck for ideas or pressed for time, a blogger can always fall back on a round-up of activity from elsewhere on the web. Yes, it’s time for a “best of the past 14 days” from the FriendFeed Life Scientists group. Just a slight twist to make it more exciting (?) – we’ll automate the process using the API and a little Ruby. #/usr/bin/ruby require "rubygems" require "json/pure" require "open-uri" bestof = JSON.parse(open("http://friendfeed-api.com/v2/feed/the-life-scientists/summary/14").read) 0.upto(9) {|entry| url = bestof['entries'][entry]['url'] body = bestof['entries'][entry]['body'] puts "<li><a href='#{url}'>ff#{entry+1}</a> - #{body}</li>" } Run, copy output and paste to ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3798733 Thu, 29 Jul 2010 07:10:20 +0100 3798733 http://www.medworm.com/index.php?rid=3946232&cid=t_104194_139_f&fid=38879&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FVirologyBlog%2F%7E3%2F8mtgBh8DCTU%2F This week’s addition to the virology toolbox was written by Chris Upton First, you may be asking yourself – Why viral bioinformatics? Good question! Although it’s true that much in the world of bioinformatics can be applied to all manner of protein and DNA sequences, there are a number of resources that are specific for viruses and there are a number of analyses that every virologist should be familiar with. So this section of the virology toolbox will highlight database resources, some useful tools and analyses, and some pitfalls you want to avoid. What do I know about viral bioinformatics? Another good question! Well, all I can say is that although I can’t program my way out of a paper bag – I’ve been analyzing DNA and protein sequences of poxvirus for 20+ years and have ... virology blog blogs http://www.medworm.com/rss/comments.php?id=3946232 Tue, 27 Jul 2010 17:13:52 +0100 3946232 http://www.medworm.com/index.php?rid=3780504&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FQ5Er_YD3QYk%2F Staying on the thirsty-topic of my earlier post, I think Pepsi contributed more to Science and related fields than most of us could. I had lost all hope that corporations could be good, but I was wrong. I don’t usually drink cola, but when I do I prefer (and always will) Pepsi. After I finish my seventh cold Pepsi can of the day (it’s hot here!) I might even want to check Science Blogs again. Cheers, with Pepsi. (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=3780504 Thu, 22 Jul 2010 22:07:40 +0100 3780504 http://www.medworm.com/index.php?rid=3780505&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2Fare8OAX5ADQ%2F have been quite late to new events, but suddenly I have an urge to drink a cold Pepsi! (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=3780505 Thu, 22 Jul 2010 20:59:29 +0100 3780505 http://www.medworm.com/index.php?rid=3767238&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F07%2F20%2Fanalysing-the-ismb-2010-meeting-using-r%2F The colossus of bioinformatics meetings, ISMB, convened in Boston this year from July 9 – 13. As in recent years, the meeting was covered online at its website, FriendFeed and Twitter. I thought it would be fun to run a quick analysis of activity at the FriendFeed room using R. 1. Fetch the data We can use the FriendFeed API to fetch data in JSON format. R provides two useful packages: RCurl, for making the HTTP request and rjson (or RJSONIO), to parse the results into a list. Since we don’t know in advance how many entries to expect, we set some arbitrarily large maximum number of entries, loop towards it and break when no more entries are returned. library(RCurl) library(rjson) ismb.url <- "http://friendfeed-api.com/v2/feed/ismb2010" ismb.data <- list() fo... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3767238 Tue, 20 Jul 2010 07:24:19 +0100 3767238 http://www.medworm.com/index.php?rid=3746908&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2F5AHh6Po1f1c%2F Viva España!! (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=3746908 Tue, 13 Jul 2010 01:08:47 +0100 3746908 http://www.medworm.com/index.php?rid=3743648&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FtDkzV3T-10M%2F 1 – The New New Thing: A Silicon Valley Story 2 – What Do You Care What Other People Think?: Further Adventures of a Curious Character 3 – Days Between Stations: A Novel 4 – A Bridge Too Far: The Classic History of the Greatest Battle of World War II 5 – The Man Who Smiled: A Kurt Wallander Mystery (4) (Vintage Crime/Black Lizard) 6 – Silence of the Grave (Reykjavik Murder Mysteries, No. 2) 7 – What Mad Pursuit: A Personal View of Scientific Discovery 8 – Seed of Light 9 – American Psycho (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=3743648 Sun, 11 Jul 2010 14:17:03 +0100 3743648 http://www.medworm.com/index.php?rid=3718624&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F07%2F02%2Fhow-many-monotypic-genera%2F During all the recent discussion around Neandertals and modern humans, it’s often pointed out that Homo sapiens is the sole extant representative of the genus Homo. I began to wonder “how unusual is this?” in a FriendFeed comment thread. What resources exist that could help us to answer this question? Genera that contain only one species are termed monotypic. Wikipedia even has a category page for this topic but their lists are limited, since Wikipedia is not a comprehensive taxonomy resource. Taxonomy is not my specialty but once in a while, I enjoy challenging myself with unfamiliar resources and data types. I figured initially that we could get some way towards an answer using BioSQL and the NCBI taxonomy database. As it turned out I was completely wrong, but it was an... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3718624 Fri, 02 Jul 2010 02:56:59 +0100 3718624 http://www.medworm.com/index.php?rid=3702972&cid=t_104194_107_f&fid=36584&url=http%3A%2F%2Fwww.biotech-weblog.com%2F50226711%2Fhuman_collagen_production_from_tobacco_plants.php © minnemomResearchers have succeeded in producing a replica of human collagen from tobacco plants, possibly making the production of commercially produced collagen for use in surgical implants and many wound healing devices in regenerative medicine. Currently, commercial collagen is produced from farm animals such as cows and pigs as well as from human cadavers and are thus prone to harbor human pathogens such as viruses or prions and, in the case of human cadavers, may possesses serious ethical issues. Producing human recombinant type I ... (Source: The Biotech Weblog) The Biotech Weblog blogs http://www.medworm.com/rss/comments.php?id=3702972 Mon, 28 Jun 2010 01:56:47 +0100 3702972 http://www.medworm.com/index.php?rid=3701782&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FI4r8gRhTk30%2F Safari 5 is the worst web browser I have ever used, IE6 included. Halting, stalling, not loading and not finding pages. A complete failure, running on OS X with all updates from the same company that programs the browser. (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=3701782 Sun, 27 Jun 2010 00:58:39 +0100 3701782 http://www.medworm.com/index.php?rid=3695607&cid=t_104194_107_f&fid=35041&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fscienceblogs%2Fdigitalbio%2F%7E3%2FPE1qQqNL5YI%2Fexploding_graphs_and_seeing_st_1.php One of my hobbies lately has been to get either RNA seq or microarray data from GEO and do quick analyses. Not only is this fun, I can find good examples to use for teaching biology. One of these fun examples comes from some Arabidopsis data. In this experiment, some poor little seedlings were taken out of their happy semi-liquid culture tubes and allowed to dry out. This simulated drought situation isn't exactly dust bowls and hollow-eyed farmers, but the plants don't know that and most likely respond in a similar way. We can get a quick idea of how the plants feel about their situation by looking at the data in a volcano plot. Read the rest of this post... | Read the comments on this post... (Source: Discovering Biology in a Digital World) Discovering Biology in a Digital World blogs http://www.medworm.com/rss/comments.php?id=3695607 Thu, 24 Jun 2010 19:49:35 +0100 3695607 http://www.medworm.com/index.php?rid=3706721&cid=t_104194_107_f&fid=36584&url=http%3A%2F%2Fwww.biotech-weblog.com%2F50226711%2Fbiomarker_for_severity_and_recurrence_of_breast_cancer.php © AmazonResearchers have identified a biomarker in the blood which can predict the severity of breast cancer in patients, distinguish breast cancer patients with a greater risk of disease recurrence, and may enable clinicians to track patients throughout the course of their treatment. The research, funded by Science Foundation Ireland (SFI) and Breast Cancer Ireland (BCI) investigated the protein changes in breast cancer that is resistant to treatment and found a higher level of a protein called HOXC11 and the presence of a secreted molecule ... (Source: The Biotech Weblog) The Biotech Weblog blogs http://www.medworm.com/rss/comments.php?id=3706721 Sat, 19 Jun 2010 02:58:29 +0100 3706721 http://www.medworm.com/index.php?rid=3671935&cid=t_104194_132_f&fid=37823&url=http%3A%2F%2Fathena.bioc.uvic.ca%2Fnode%2F1078 NEBC Homepage — NERC Environmental Bioinformatics Centre Bio-Linux 6.0 (http://nebc.nerc.ac.uk/tools/bio-linux) featured in Canadian Bioinformatics Helpdesk Newsletter From their site: read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=3671935 Fri, 18 Jun 2010 02:14:41 +0100 3671935 http://www.medworm.com/index.php?rid=3662848&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2F5FWb2K-jBAo%2F Some irrelevant impressions about the World Cup in South Africa: - vuvuzela will probably be the only thing that you will remember about this cup. And that’s sad. - mediocre players so far (with few exceptions), mediocre ball - According to CBC (Canada) Australia is (was) one the coming powers in football. I guess they need to hire some real analysts, or let me comment hockey - Apart from Messi and Germany, nothing good so far. And the English goalkeeper too, classic. It’s becoming a norm to make fun of the poor Englishmen every four years. - Also according to Canadian TV, Italy is not known for slow starts. They don’t have tapes from the matches since 1982. Again, better analysts. (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=3662848 Mon, 14 Jun 2010 23:51:54 +0100 3662848 http://www.medworm.com/index.php?rid=3635964&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F06%2F07%2Fbiomart-and-genomegraphs-a-worked-example%2F As promised a few posts ago, another demonstration of the excellent biomaRt package, this time in conjunction with GenomeGraphs. Here’s what we’re going to do: Grab some public microarray data Normalise and get a list of the most differentially-expressed probesets Use biomaRt to fetch the genes associated with those probesets Plot the data using GenomeGraphs If you want to follow along on your own machine, it will need to be quite powerful. We’ll be processing exon arrays, which requires a 64-bit machine with at least 4 GB (and preferably, at least 8-12 GB) of RAM. As usual, I’m assuming some variant of Linux and that you’re comfortable at the command line. 1. The data First, grab your raw data. In this example, we’ll use GEO series GSE12236, titled &... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3635964 Mon, 07 Jun 2010 02:10:47 +0100 3635964 http://www.medworm.com/index.php?rid=3625705&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FnWj6DyT_SGM%2F About a year ago I purchased Zennaware‘s Cornerstone, a SVN client for Macs. It’s a nice application, works really well, it does what it is supposed to do, But as any software is has bugs and problems, and after paying around 50 bucks for a license, one expects that at least one email asking how perform one thing with the software would be answered. It has been more than three weeks that I sent an email to their support team in order to know how to delete some failed repositories from a list, still nothing. Sometimes, I don’t know why I pay for software. (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=3625705 Wed, 02 Jun 2010 15:59:43 +0100 3625705 http://www.medworm.com/index.php?rid=3599474&cid=t_104194_107_f&fid=36584&url=http%3A%2F%2Fwww.biotech-weblog.com%2F50226711%2Fdna_vaccine_against_dll4_protein_slows_down_cancer.php © WIkipediascientists at the Karolinska Institutet have a developed a DNA vaccine targeted at a protein known as 'Delta-like ligand 4' (DLL4), which has recently been identified as an important component in regulating the formation of new blood vessels. By blocking the expression of DLL4 in a tumour, new, but non-functional, blood vessels, are formed, slowing down tumor growth. Results from an animal trial have shown that vaccination against DLL4 causes an immunological antibody response to DLL4, hindering the growth of breast cancer in ... (Source: The Biotech Weblog) The Biotech Weblog blogs http://www.medworm.com/rss/comments.php?id=3599474 Wed, 26 May 2010 01:04:00 +0100 3599474 http://www.medworm.com/index.php?rid=3592356&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F05%2F24%2Fif-you-must-send-me-an-excel-spreadsheet%2F …please, try to follow these simple guidelines. 1. Don’t bother to format the cells Where possible, I will not open your spreadsheet in a spreadsheet application. If I do, it will be only to marvel at the horror, then export it as rapidly as possible to a delimited text file. I do not care about the font, the font size or the font weight. I do not care whether there are grid lines around the cells. I especially do not care about cells which you have highlighted using some arbitrary (and unexplained) colour scheme. 2. No multiple tables If you include multiple “tables” on one sheet, separated by blank rows, there is a good chance that I will not notice them. If you include multiple tables on multiple “sheets”, there is an excellent chance that I will not ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3592356 Mon, 24 May 2010 06:33:57 +0100 3592356 http://www.medworm.com/index.php?rid=3573865&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F05%2F18%2Fdata-management-its-funny-because-its-true%2F Please read My Data Management Plan – a satire Have a good giggle Ask yourself if anything sounds familiar If you answered yes to (3), do something about it That is all. Filed under: bioinformatics, blogroll, computing, programming Tagged: best practice, data management, humour, satire (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3573865 Tue, 18 May 2010 01:52:43 +0100 3573865 http://www.medworm.com/index.php?rid=3570009&cid=t_104194_132_f&fid=35021&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FYourBonesGotALittleMachine%2F%7E3%2FO4btHltj2IM%2F Recently I’ve noticed the emergence of several Stack Overflow-style sites for science-related questions and answers. For those unfamiliar with Stack Overflow – it’s a question and answer ‘forum’ for computer programmers that keeps the signal-to-noise ratio very high through a carefully refined reputation system. Late last year the creators of Stack Overflow launched a hosted service called Stack Exchange, which allows anyone to start their own “Stack Overflow” based around any topic. http://www.flickr.com/photos/alicebartlett/ / CC BY-NC 2.0 The service is was a little pricey ($129+/month), and I suspect this is one reason why a few open source clones inspired by Stack Overflow also exist. Since then, Stack Exchange sites (or clones) have prolifer... Your bones got a little machine. blogs http://www.medworm.com/rss/comments.php?id=3570009 Wed, 12 May 2010 05:33:48 +0100 3570009 http://www.medworm.com/index.php?rid=3556283&cid=t_104194_132_f&fid=35021&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FYourBonesGotALittleMachine%2F%7E3%2FO4btHltj2IM%2F Recently I’ve noticed the emergence of several Stack Overflow-style sites for science-related questions and answers. For those unfamiliar with Stack Overflow – it’s a question and answer ‘forum’ for computer programmers that keeps the signal-to-noise ratio very high through a carefully refined reputation system. Late last year the creators of Stack Overflow launched a hosted service called Stack Exchange, which allows anyone to start their own “Stack Overflow” based around any topic. http://www.flickr.com/photos/alicebartlett/ / CC BY-NC 2.0 The service is was a little pricey ($129+/month), and I suspect this is one reason why a few open source clones inspired by Stack Overflow also exist. Since then, Stack Exchange sites (or clones) have prolifer... Your bones got a little machine. blogs http://www.medworm.com/rss/comments.php?id=3556283 Wed, 12 May 2010 05:33:48 +0100 3556283 http://www.medworm.com/index.php?rid=3569861&cid=t_104194_107_f&fid=36584&url=http%3A%2F%2Fwww.biotech-weblog.com%2F50226711%2Fgenetic_variations_linked_to_caries_and_gum_disease.php © robtxgalDental school researchers have found out that certain genetic variations may be linked to higher rates of tooth decay and aggressive periodontitis. Apparently, the rate of dental caries was influenced by individual variations, or polymorphisms, in a gene called beta defensin 1 (DEFB1), which plays a key role in the first-line immune response against invading germs. For the study, the researchers analyzed nearly 300 dental records and accompanying saliva samples, and assigned each case a DMFT score based on the presence of decayed ... (Source: The Biotech Weblog) The Biotech Weblog blogs http://www.medworm.com/rss/comments.php?id=3569861 Mon, 03 May 2010 02:31:58 +0100 3569861 http://www.medworm.com/index.php?rid=3526898&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2F38EsYAhVhIo%2F So, says Twitter: (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=3526898 Sun, 02 May 2010 23:34:04 +0100 3526898 http://www.medworm.com/index.php?rid=3522772&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FifqXVsNWZMQ%2F This week in a public speech the individual that acts as Brazilian president uttered the following gem (loosely translated by me): We are the result of a triple mixture, I mean, a genetics purified in three continents that resulted in our people. I don’t know if there’s another people (nation) like us, but there’s nothing better, nothing more pure than us For those who think living under Bush (and Harper to some extent) was cruel, I don’t want to imagine what is to live being governed by this idiot. (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=3522772 Fri, 30 Apr 2010 19:02:14 +0100 3522772 http://www.medworm.com/index.php?rid=3515556&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FBHC5oX07zs4%2F 1 – The New New Thing: A Silicon Valley Story 2 – What Do You Care What Other People Think?: Further Adventures of a Curious Character 3 – Days Between Stations: A Novel 4 – A Bridge Too Far: The Classic History of the Greatest Battle of World War II 5 – The Man Who Smiled: A Kurt Wallander Mystery (4) (Vintage Crime/Black Lizard) 6 – Silence of the Grave (Reykjavik Murder Mysteries, No. 2) (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=3515556 Wed, 28 Apr 2010 20:42:58 +0100 3515556 http://www.medworm.com/index.php?rid=3463629&cid=t_104194_107_f&fid=36584&url=http%3A%2F%2Fwww.biotech-weblog.com%2F50226711%2Fpatient_genetics_and_warfarin_coumadin_dosing.php © gregor_yPrevious studies have indicated that individual genetic variation affects how warfarin is tolerated and broken down by the body, and scientists have developed several formulas that take genetic information into account when calculating warfarin dosage. Now, a five-year, $3.7 million clinical trial is underway to investigate a formula that includes three gene variations that have been shown to influence a person's warfarin sensitivity or metabolism. "Without any anticoagulant, orthopedic patients have a nearly 50 percent chance of having a blood clot after hip ... (Source: The Biotech Weblog) The Biotech Weblog blogs http://www.medworm.com/rss/comments.php?id=3463629 Tue, 13 Apr 2010 07:23:51 +0100 3463629 http://www.medworm.com/index.php?rid=3449066&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2Ft_vBjvNulMY%2F And a lot of it, but not to buy larger machines, or to create big departments or institute. Not even research investment. Bioinformatics needs investment in people, in courses, in workshops, in good practices for software development, in a knowledge base. Although, some people said sometime ago that “Bioinformatics is (was) dead”, the future is only bioiformatical ®. When was the last time you saw a bank branch with no computers? (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=3449066 Wed, 07 Apr 2010 18:56:14 +0100 3449066 http://www.medworm.com/index.php?rid=3443921&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FO-NX4pIi3KM%2F Open Science is like pregnancy: either you are or you are not. There’s no sort-of Open Science, as there’s no sort-of pregnant woman. (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=3443921 Wed, 07 Apr 2010 03:05:04 +0100 3443921 http://www.medworm.com/index.php?rid=3436361&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FYUeU7wWfKEA%2F Image via CrunchBase No, I don’t pirate them either. But whenever I buy something I get highly disappointed. Recently I bought TuneUp, which is a iTunes plugin for Macs. It seems to work great, most of the time at least, bu every time I add one song to the library, it tries to re-sync with it, and it usually takes hours and hours. Really frustrating. That’s why is better to stick to free stuff and donate when you feel like doing it. Sometimes it’s better. (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=3436361 Sun, 04 Apr 2010 13:14:02 +0100 3436361 http://www.medworm.com/index.php?rid=3411233&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FyDriPchI5bY%2F Image via Wikipedia This year during the Earth Hour (I don’t know when it is), I will leave all my EnergyStar ® appliances on, including my gas-powered alarm clock. (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=3411233 Fri, 26 Mar 2010 18:52:37 +0100 3411233 http://www.medworm.com/index.php?rid=3395178&cid=t_104194_107_f&fid=36584&url=http%3A%2F%2Fwww.biotech-weblog.com%2F50226711%2Fyou_test_youtm_cancer_assessment_kit.php Nowadays it is possible for an individuals to detect if they have cancer while it is in its early stages without even having to make an appointment with a own doctor. Whether it's due to a general anxiety about developing cancer or increased exposure to risk factors associated with cancer, an individual can now have answers with the You Test YouTM Cancer Assessment kit. The test kit measures a marker called tFFDP (tumor fibrin and fibrinogen degradation products), which is associated with 18 different ... (Source: The Biotech Weblog) The Biotech Weblog blogs http://www.medworm.com/rss/comments.php?id=3395178 Sat, 13 Mar 2010 19:17:52 +0100 3395178 http://www.medworm.com/index.php?rid=3298516&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FoakDTIefvZQ%2F I have been invited by Packt Publishing to review Python Testing Beginner’s Guide. You can take a look at the preview here and even download one chapter of the book. (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=3298516 Mon, 22 Feb 2010 18:22:14 +0100 3298516 http://www.medworm.com/index.php?rid=3283768&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FmRlasdfh30Q%2F Image via Wikipedia I’m buying a front row seat to every event in the London’s 2012 Olympics, even at the simultaneous ones (I will figure out cloning by then), and I will report every small glitch th happens there. Still on the topic, how come a country/city/whatever that designed that logo can criticize anyone, ever, in any subject of modern and past life? Related articles by Zemanta Gold for whining goes to… British reporters (calgaryherald.com) UK/Canada Spat Uncharacteristically Crude, Penis-Related [Media Meltdowns] (deadspin.com) (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=3283768 Thu, 18 Feb 2010 14:47:39 +0100 3283768 http://www.medworm.com/index.php?rid=3280147&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FLetmYDsW9DQ%2F 1 – The New New Thing: A Silicon Valley Story 2 – What Do You Care What Other People Think?: Further Adventures of a Curious Character 3 – Days Between Stations: A Novel 4 – A Bridge Too Far: The Classic History of the Greatest Battle of World War II (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=3280147 Wed, 17 Feb 2010 14:48:29 +0100 3280147 http://www.medworm.com/index.php?rid=3223442&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F01%2F30%2Fismb-2009-reports%2F Great to see more reports describing the use of online tools to cover scientific meetings. Here are the publications, from PLoS Computational Biology: Live Coverage of Scientific Conferences Using Web Technologies. doi:10.1371/journal.pcbi.1000563 Live Coverage of Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB) 2009. doi:10.1371/journal.pcbi.1000640 And here’s Ally a.k.a the robo-blogger on Social Networking and Guidelines for Life Science Conferences. Looks like we’ve started a trend, long may it continue at future meetings. Filed under: bioinformatics, meetings, publications Tagged: 2009, eccb, friendfeed, ismb, report (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3223442 Sat, 30 Jan 2010 04:22:12 +0100 3223442 http://www.medworm.com/index.php?rid=3223443&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F01%2F30%2Fphosphogrid%2F I no longer work on protein kinases but when I did, PhosphoGRID is the kind of database that I would have wanted to see. It features: A nice clean interface, with good use of Javascript Useful information returned from a simple search form Data for download in plain text format with no restrictions or requirements for registration All it lacks is a RESTful API, but nothing is perfect :-) Published in the little-known but often-useful journal Database: PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae. doi:10.1093/database/bap026. Filed under: bioinformatics, publications, web resources Tagged: database, phosphory, protein kinases (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3223443 Sat, 30 Jan 2010 04:10:45 +0100 3223443 http://www.medworm.com/index.php?rid=3216779&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FsFZ3zUUPyTU%2F Just sayin’. With all the negative reviews, ponderations, blog posts, newspaper reports, I just wanted to give so kudos to Steve and the Apple family. Is it the best product ever? No. Is it the next coming of Jesus Christ? No. So what is it? It’s just another product, and you, only you (maybe with your wife/husband/partner/household) will decide if it fits your budget, if it is useful for you and if you actually need to buy it. Apart from that, rants are always good for the people that writes them (I know it firsthand). The icing on the cake is when I overheard two homeless guys discussing if you could multitask on an iPad. When they discovered you couldn’t, they decided not to buy it. Last time I saw them they were in the public library computers. (Source: Blind.Scientis... Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=3216779 Thu, 28 Jan 2010 15:08:17 +0100 3216779 http://www.medworm.com/index.php?rid=3216781&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2F7wm6Opo7134%2F I’m reading the second book on Feynman, What Do You Care What Other People Think?: Further Adventures of a Curious Character and the only thing I can he was an incredible person, one that any one can admire. I have no idols, I don’t worship anyone, but Feynman gets the closest possible to being one for me. (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=3216781 Thu, 28 Jan 2010 01:40:01 +0100 3216781 http://www.medworm.com/index.php?rid=3212505&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F01%2F27%2Fclustering-geo-samples-by-title-briefly-revisited%2F So, we had a brief discussion regarding my previous post and clearly the statement: The longest key for which values exist classifies your titles does not hold true for all cases. Not that I ever said that it did! I remind you that this blog is a place for the half-formed ideas that spill out of my head, not an instruction manual. Let’s look, for example, at GSE19318. This GEO series comprises 2 platforms: one for dog (10 samples) and one for humans (1 sample), with these sample titles: ['Dog-tumor-81705', 'Dog-tumor-78709', 'Dog-tumor-88012', 'Dog-tumor-8888302', 'Dog-tumor-209439', 'Dog-tumor-212227', 'Dog-tumor-48', 'Dog-tumor-125', 'Dog-tumor-394', 'Dog-tumor-896', 'Human-tumor'] Run that through the Ruby code in my last post and we get: {"Dog-tumor-48"=>["... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3212505 Wed, 27 Jan 2010 01:29:56 +0100 3212505 http://www.medworm.com/index.php?rid=3201861&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F01%2F24%2Fthinking-algorithmically-clustering-geo-samples-by-title%2F Today’s challenge. Take a look at this array, which contains the “title” field for the 6 samples from GSE1323, a series in the GEO microarray database: ['SW-480-1','SW-480-2','SW-480-3','SW-620-1','SW-620-2','SW-620-3'] Humans are very good at classification. Almost instantly, you’ll see that there are 2 classes, “SW-480″ and “SW-620″, each with 3 samples. How can we write a program to do the same job? I’m sure that for those with formal training in computer science and algorithms, this is pretty trivial. The rest of us have to figure it out from first principles. Here’s what I did, in words: # Imagine that you have 2 titles: "abc1" and "abc2" # Take the first character - call it the key, call the remaining... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3201861 Sun, 24 Jan 2010 05:03:00 +0100 3201861 http://www.medworm.com/index.php?rid=3200613&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FL7-3Lnya21k%2F Seven months of fun, barely missed one episode. (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=3200613 Sat, 23 Jan 2010 13:47:10 +0100 3200613 http://www.medworm.com/index.php?rid=3200614&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FsJd0W289ldM%2F from Toronto’s (GTA’s) streets for sometime. Twelve people died crossing the streets this year in the region. Stay away. (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=3200614 Fri, 22 Jan 2010 19:22:10 +0100 3200614 http://www.medworm.com/index.php?rid=3193945&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FK4-02G3tztU%2F That works for me, maybe not for you. And that is where the mask of Canadian-style humility and niceness came off James Cameron, the engineer’s son from Kapuskasing, and the scarily arrogant, tactless King of the World (as he called himself at the 1998 Oscar show) slipped out. (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=3193945 Tue, 19 Jan 2010 17:51:05 +0100 3193945 http://www.medworm.com/index.php?rid=3182210&cid=t_104194_107_f&fid=36584&url=http%3A%2F%2Fwww.biotech-weblog.com%2F50226711%2Fgenomics_of_sunflower.php © Esdras CalderanGenome Canada, Genome BC, US Departments of Energy and Agriculture, and France's INRA (National Institute for Agricultural Research) has undertaken a US$10.5 million research project that will create a reference genome for the sunflower family - currently the world's largest plant family, containing 24,000 species of plants, including many crops, medicinal plants, horticulture plants and noxious weeds. Th project, titled Genomics of Sunflower, will use next-generation genotyping and sequencing technologies to sequence, assemble and annotate the sunflower genome and to locate the ... (Source: The Biotech Weblog) The Biotech Weblog blogs http://www.medworm.com/rss/comments.php?id=3182210 Sun, 17 Jan 2010 15:57:57 +0100 3182210 http://www.medworm.com/index.php?rid=3171934&cid=t_104194_107_f&fid=35041&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fscienceblogs%2Fdigitalbio%2F%7E3%2FkXlP72IPp4I%2Fcitizen_science_and_digital_bi.php Is there a place for citizen scientists in the world of digital biology? Many of the citizen science projects that I've been reading about have a common structure. There's a University lab at the top, outreach educators in the middle, and a group of citizens out in the field collecting data. After the data are collected, they end up in a database somewhere and the University researchers analyze them and write papers. At least that's my impression so far. It seems to me, that with all kinds of databases out there, on-line, there should be plenty of opportunity for both citizens and student groups to participate in analyzing the data. But do they? #scio10 Read the rest of this post... | Read the comments on this post... (Source: Discovering Biology in a Digital World) Discovering Biology in a Digital World blogs http://www.medworm.com/rss/comments.php?id=3171934 Wed, 13 Jan 2010 20:11:25 +0100 3171934 http://www.medworm.com/index.php?rid=3163976&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F01%2F12%2Fa-new-twist-on-the-identifier-mapping-problem%2F Yesterday, Deepak wrote about BridgeDB, a software package to deal with the “identifier mapping problem”. Put simply, biologists can name a biological entity in any way that they like, leading to multiple names for the same object. Easily solved, you might think, by choosing one identifier and sticking to it, but that’s apparently way too much of a challenge. However, there are times when this situation is forced upon us. Consider this code snippet, which uses the Bioconductor package GEOquery via the RSRuby library to retrieve a sample from the GEO database: require "rubygems" require "rsruby" if ENV['R_HOME'].nil? ENV['R_HOME'] = "/usr/lib/R" end r = RSRuby.instance r.library("GEOquery") sample = r.getGEO("GSM434143"... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3163976 Tue, 12 Jan 2010 03:57:02 +0100 3163976 http://www.medworm.com/index.php?rid=3156495&cid=t_104194_107_f&fid=35041&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fscienceblogs%2Fdigitalbio%2F%7E3%2FSxT42S-NrNU%2Fin_the_cloud_next_gen_dna_sequ.php These days, DNA sequencing happens in one of three ways. In the early days of DNA sequencing (like the 80's), labs prepared their own samples, sequenced those samples, and analyzed their results. Some labs still do this. Then, in the 90's, genome centers came along. Genome centers are like giant factories that manufacture sequence data. They have buildings, dedicated staff, and professional bioinformaticians who write programs and work with other factory members to get the data entered, analyzed, and shipped out to the databases. (You can learn more about this and go on a virtual tour in this nice video from Washington University). At the same time, Universities expanded their core service laboratories and these labs began offering a greater number of sequencing services. Today, much t... Discovering Biology in a Digital World blogs http://www.medworm.com/rss/comments.php?id=3156495 Fri, 08 Jan 2010 23:24:50 +0100 3156495 http://www.medworm.com/index.php?rid=3153558&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F01%2F08%2Fsamples-per-seriesdataset-in-the-ncbi-geo-database%2F Andrew asks: I want to get an NCBI GEO report showing the number of samples per series or data set. Short of downloading all of GEO, anyone know how to do this? Is there a table of just metadata hidden somewhere? At work, we joke that GEO is the only database where data goes in, but it won’t come out. However, there is an alternative: the GEOmetadb package, available from Bioconductor. The R code first, then some explanation: # install GEOmetadb source("http://bioconductor.org/biocLite.R") biocLite("GEOmetadb") library(GEOmetadb) # connect to database getSQLiteFile() con <- dbConnect(SQLite(), "GEOmetadb.sqlite") # count samples per GDS gds.count <- dbGetQuery(con, "select gds,sample_count from gds") gds.count[1:5,] # first 5 results... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3153558 Fri, 08 Jan 2010 01:01:09 +0100 3153558 http://www.medworm.com/index.php?rid=3142760&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2F7XMWjSVfjFI%2F Post of the day is the phrase of the day, overheard online in an interview on the Brazilian TV channel, Globo News: “(…) Brazil’s urban planning is prehistorical (…)”. I can say that not only urban planning is prehistorical. (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=3142760 Tue, 05 Jan 2010 00:33:23 +0100 3142760 http://www.medworm.com/index.php?rid=3136579&cid=t_104194_107_f&fid=35041&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fscienceblogs%2Fdigitalbio%2F%7E3%2FnESR_qzlURQ%2Fa_biologist_by_yet_another_nam.php What do you call a biologist who uses bioinformatics tools to do research, but doesn't program? You don't know? Neither does anyone else. Read the rest of this post... | Read the comments on this post... (Source: Discovering Biology in a Digital World) Discovering Biology in a Digital World blogs http://www.medworm.com/rss/comments.php?id=3136579 Sat, 02 Jan 2010 00:39:07 +0100 3136579 http://www.medworm.com/index.php?rid=3135661&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2Fy99MH6g-P8M%2F I plan to post 365 entries either here, here or here in 2010. I might not post everyday, but I will try to keep the mark, even if it’s only a one-liner or some link to interesting news/software/paper. Happy New Year everyone! (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=3135661 Fri, 01 Jan 2010 15:37:04 +0100 3135661 http://www.medworm.com/index.php?rid=3133755&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FCYaPJ1Ec8-0%2F Friends, as the year draws to a close, I felt compelled to compile the best of the decade of 00s. The list is: will be posted here as soon as the decade ends on Dec 31st, 2010. (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=3133755 Thu, 31 Dec 2009 03:37:38 +0100 3133755 http://www.medworm.com/index.php?rid=3133623&cid=t_104194_107_f&fid=35041&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fscienceblogs%2Fdigitalbio%2F%7E3%2FrttFGfgabY8%2Fone_for_the_tool_builders.php I often get questions about bioinformatics, bioinformatics jobs and career paths. Most of the questions reflect a general sense of confusion between creating bioinformatics resources and using them. Bioinformatics is unique in this sense. No one confuses writing a package like Photoshop with being a photographer, yet for some odd reason, people seem to expect this of biologists. In the same respect, even the programmers and database administrators who work in bioinformatics, are unfairly assumed to have had graduate level training in biology. In many ways, it's easiest to understand what bioinformatics is, and to choose a bioinformatics-related career, by dividing the field's participants into two groups: the tool builders and the tool users. The tool builders are the programmers, archi... Discovering Biology in a Digital World blogs http://www.medworm.com/rss/comments.php?id=3133623 Wed, 30 Dec 2009 20:49:46 +0100 3133623 http://www.medworm.com/index.php?rid=3106853&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2F52e7yywUbek%2F Here’s the best and worst of 2009: - Movie: Rockrolla, not the best one, but highly entertaining, worst: Funny People - Book: Born Standing Up: A Comic’s Life by Steve Martin, highly entertaining too - Website: The Secret Diary of Steve Jobs, worst: of the ones I usually read is the Daring Fireball - Software: Textmate, worst Mendeley, by 1000 miles - TV: Stephen Colbert and Jon Stewart, the best hour of TV, worst: Dexter’s finale - Purchase: MacBook 13”, the best computer I ever had - Money-grabbing-scheme: Global Warming or Climate Change - Politician: no best in the category, but the worst is the Brazilian President. - Music: I didn’t have a favourite this year. but Matthew Good’s Vancouver is growing on me. No worst, or too many to care about - Best ... Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=3106853 Sun, 20 Dec 2009 00:55:53 +0100 3106853 http://www.medworm.com/index.php?rid=3122099&cid=t_104194_107_f&fid=36584&url=http%3A%2F%2Fwww.biotech-weblog.com%2F50226711%2Fpeptide_identifies_tumors_and_penetrates_to_deliver_anticancer_compounds.php © kaibara87Researchers at Burnham Institute for Medical Research have identified a new peptide called iRGD that specifically recognizes and penetrates cancer tumors but not normal tissues. The peptide was also shown to deliver diagnostic particles and medicines into the tumor. This discovery stems from the previous discovery of "vascular zip codes," which showed that blood vessels in different tissues (including diseased tissues) have different signatures. These signatures can be detected and used to dock drugs onto vessels inside the diseased tissue. In addition to ... (Source: The Biotech Weblog) The Biotech Weblog blogs http://www.medworm.com/rss/comments.php?id=3122099 Tue, 08 Dec 2009 14:09:13 +0100 3122099 http://www.medworm.com/index.php?rid=3122100&cid=t_104194_107_f&fid=36584&url=http%3A%2F%2Fwww.biotech-weblog.com%2F50226711%2Fsoy_peptide_lunasin_has_anticancer_antiinflammatory_properties.php © Kanko*Two studies report that lunasin, a soy peptide present in effluents from soy-processing plants, may have important health benefits that include fighting leukemia and blocking the inflammation that accompanies such chronic health conditions as diabetes, heart disease, and stroke. In the cancer study, de Mejia's group identified a key sequence of amino acids—arginine, glycine, and aspartic acid, (the RGD motif)—that triggered the death of leukemia cells by activating a protein called caspase-3. "Other scientists have noted the cancer-preventive effects of the RGD ... (Source: The Biotech Weblog) The Biotech Weblog blogs http://www.medworm.com/rss/comments.php?id=3122100 Wed, 02 Dec 2009 14:57:39 +0100 3122100 http://www.medworm.com/index.php?rid=3048146&cid=t_104194_107_f&fid=35041&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fscienceblogs%2Fdigitalbio%2F%7E3%2FItfpSQ0y3NI%2Fnext_generation_dna_sequencing_1.php For many years, I've been perfectly content to work with small numbers of things. Working with one gene or one protein is great. Even small groups of genes are okay. I'm fine with alternatively spliced genes with multiple transcripts, or multiple polymorphisms, or genes in multi-gene families, or groups of genes in operons. But I never trusted microarrays. Read the rest of this post... | Read the comments on this post... (Source: Discovering Biology in a Digital World) Discovering Biology in a Digital World blogs http://www.medworm.com/rss/comments.php?id=3048146 Wed, 02 Dec 2009 14:21:22 +0100 3048146 http://www.medworm.com/index.php?rid=3048289&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F12%2F02%2Fhas-our-quest-for-completeness-made-things-too-complicated%2F In my opinion, yes. Let me elaborate. My current job is very much focused on “data integration”. What this means is that we have a large amount of diverse data from different “-omics” experiments: microarrays, protein mass spectrometry, DNA sequencing – really, whatever you like, but it’s all aimed at answering the same question. Namely: which of these biological entities (transcripts, proteins, metabolites) are markers for various human disease states? Somehow, we have to pull all of these data into a common framework so that it can be analysed using statistics. The problem: whilst a lot of effort has gone into designing schema and ontologies that describe the individual data types, less effort has been applied to the question: what do all these things... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3048289 Wed, 02 Dec 2009 02:38:06 +0100 3048289 http://www.medworm.com/index.php?rid=3030034&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2Fv5mHDKYmEjw%2F Image via Wikipedia Yes, DIALIGN-TX has all the problems with scientific software. All of them in 1.8 Mb of data, and I’m being kind. Let me explain that. I have this small project, and DIALIGN-TX is one of the programs I want to check. I compiled fine, or so I think: it runs ok on the Mac, shows me the parameters to run it, in a large list of options. Most of these options have a “DEFAULT” value, which means they are not needed to run the program. And there’s an usage example Usage: dialign-t [OPTIONS] [] (notice the error on the usage, I just copied and pasted) I tried every possible combination, with and without options, setting and not setting them, with different input files, no one worked. Then I decided to read the documentation. No true. First I decided ... Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=3030034 Thu, 26 Nov 2009 14:21:06 +0100 3030034 http://www.medworm.com/index.php?rid=3026637&cid=t_104194_87_f&fid=34765&url=http%3A%2F%2Fhcrenewal.blogspot.com%2F2009%2F11%2Fmerck-seeks-medical-informatics-loser.html P { MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px } BODY { SCROLLBAR-ARROW-COLOR: #3f52b8; SCROLLBAR-DARKSHADOW-COLOR: #fafafa; SCROLLBAR-BASE-COLOR: #f7f7f7; SCROLLBAR-HIGHLIGHT-COLOR: #cecfce; SCROLLBAR-TRACK-COLOR: #fffbff } At the post "Medical Informatics, Pharma, Health IT, and Golden Advice That Sits Sadly Unused" and other posts I lamented the fact that the pharma sector (in deep decline due to scientific mediocrity, ill-qualified leadership, public image tarnished by scandal, and other reasons), as well as the Healthcare IT industry (now also racked by similar issues and undergoing a Senate investigation while its products are being found to show little benefit) neglected a scientific discipline that might actually help them achieve the goals of better products, better patient care, and str... Health Care Renewal blogs http://www.medworm.com/rss/comments.php?id=3026637 Tue, 17 Nov 2009 01:00:00 +0100 3026637 http://www.medworm.com/index.php?rid=3003702&cid=t_104194_87_f&fid=34765&url=http%3A%2F%2Fhcrenewal.blogspot.com%2F2009%2F11%2Fmerck-seeks-medical-informatics-loser.html P { MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px } BODY { SCROLLBAR-ARROW-COLOR: #3f52b8; SCROLLBAR-DARKSHADOW-COLOR: #fafafa; SCROLLBAR-BASE-COLOR: #f7f7f7; SCROLLBAR-HIGHLIGHT-COLOR: #cecfce; SCROLLBAR-TRACK-COLOR: #fffbff } At the post "Medical Informatics, Pharma, Health IT, and Golden Advice That Sits Sadly Unused" and other posts I lamented the fact that the pharma sector (in deep decline due to scientific mediocrity, ill-qualified leadership, public image tarnished by scandal, and other reasons), as well as the Healthcare IT industry (now also racked by similar issues and undergoing a Senate investigation while its products are being found to show little benefit) neglected a scientific discipline that might actually help them achieve the goals of better products, better patient care, and str... Health Care Renewal blogs http://www.medworm.com/rss/comments.php?id=3003702 Tue, 17 Nov 2009 01:00:00 +0100 3003702 http://www.medworm.com/index.php?rid=2999483&cid=t_104194_87_f&fid=34765&url=http%3A%2F%2Fhcrenewal.blogspot.com%2F2009%2F11%2Fmerck-seeks-medical-informatics-loser.html P { MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px } BODY { SCROLLBAR-ARROW-COLOR: #3f52b8; SCROLLBAR-DARKSHADOW-COLOR: #fafafa; SCROLLBAR-BASE-COLOR: #f7f7f7; SCROLLBAR-HIGHLIGHT-COLOR: #cecfce; SCROLLBAR-TRACK-COLOR: #fffbff } At the post "Medical Informatics, Pharma, Health IT, and Golden Advice That Sits Sadly Unused" and other posts I lamented the fact that the pharma sector (in deep decline due to scientific mediocrity, ill-qualified leadership, public image tarnished by scandal, and other reasons), as well as the Healthcare IT industry (now also racked by similar issues and undergoing a Senate investigation while its products are being found to show little benefit) neglected a scientific discipline that might actually help them achieve the goals of better products, better patient care, and str... Health Care Renewal blogs http://www.medworm.com/rss/comments.php?id=2999483 Tue, 17 Nov 2009 01:00:00 +0100 2999483 http://www.medworm.com/index.php?rid=2970358&cid=t_104194_132_f&fid=35001&url=http%3A%2F%2Farchive.nodalpoint.org%2F2009%2F11%2F06%2Fduncan_hulls_blog_has_moved If you're here looking for Duncan Hull's blog, it has moved to O'Really?. Nodalpoint lives on at nodalpoint.org. (Source: nodalpoint.org - A bioinformatics weblog) nodalpoint.org - A bioinformatics weblog blogs http://www.medworm.com/rss/comments.php?id=2970358 Fri, 06 Nov 2009 20:26:55 +0100 2970358 http://www.medworm.com/index.php?rid=2851984&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FSNB0_8mLGAU%2F I have two Google Wave invites to go. If you want one send me an email (paulo.nuin on Gmail) or leave a comment here. The best “offer” takes it. Offer means anything: a poem, a sticker, another invite to another service, a scientific collaboration, anything. Be creative and you will have it. Update: I will send both invites later tonight, Canada’s ET. Google says it might take a while for the invite to reach the recipient. Some people are selling invites on Ebay, some for 100 dollars. Again the best “offer” wins. And remember, I’m not checking Twitter or Friendfeed. (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=2851984 Thu, 01 Oct 2009 14:12:26 +0100 2851984 http://www.medworm.com/index.php?rid=2851968&cid=t_104194_131_f&fid=34989&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FGeneticsHealth%2F%7E3%2Fd0tjpkB_Oss%2F Music and cancer do not go together, and I mean that in the context of this new technology: A project at Harvard Medical School created a program to translate the signals from cells into musical notes. Normal signals will sound harmonious, abnormal signals like those coming from cancer cells will sound awful. Listen to this –     Using date from a pre-existing colon cancer study, bioinformatician Gil Alterovitz and his team created a program that transforms complex genomic information into musical notes, so that abnormal data will sound discordant. “When things go awry, such as in the case of p53-null mutant colon cancer cells under inflammatory stress conditions, gene expression varies slightly, and inharmonious chord progressions result. Listening to the result... Genetics and Health blogs http://www.medworm.com/rss/comments.php?id=2851968 Wed, 30 Sep 2009 20:11:20 +0100 2851968 http://www.medworm.com/index.php?rid=2851985&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FiXB2IuhcykA%2F There has been a somewhat heated debate in Roderic Page’s blog about Mendeley’s hype in the current reference management scenario. Also, I was forwarded to this blog post, which praises the right horse in the ref-management race, Zotero. The comments in that post are pure gold, showing how PR in science is pernicious to science itself. I will give two examples. For those who don’t know, I’m one of the poster-boys of the anti-Mendeley movement. Not because I want to be a poster-boy, but because I’m not afraid to confront their PR machine, even more after the censorship attempt. One of the worst aspects of this efficient PR machine is to use scientists to inflate the hype on the so-called social media websites, and answer everyone that might be criticizing the ... Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=2851985 Wed, 30 Sep 2009 20:00:55 +0100 2851985 http://www.medworm.com/index.php?rid=2842719&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2Fdcg7PDsvIzo%2F to “social websites”. Yes, this is a farewell to my two readers and the handful of people that read my tweets/friendfeed posts. I’m not going away, everything is still going to be channeled through FriendFeed, and posted on Twitter, but I won’t comment anymore or actually write them. It will be automatic, and personal to the level where it’s generated by my selections, not meaning they are good or bad, right or wrong, just that whatever caught my eye. I will still write here, have my Facebook account and the other “social” things, but myself, I’ll be gone. There’s a feeling of deja vu writing this, I feel that I’ve written this before, but this time it’s true and definitive. I need to focus on my work, and got tired of the ... Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=2842719 Mon, 28 Sep 2009 20:46:34 +0100 2842719 http://www.medworm.com/index.php?rid=2823675&cid=t_104194_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2009%2F09%2Fmetaproteomics.html Microbial ecology is currently experiencing a renaissance spurred by the rapid development of molecular techniques and "omics" technologies in particular. As never before, these tools have allowed researchers in the field to produce a massive amount of information through in situ measurements and analysis of natural microbial communities, both vital approaches to the goal of unraveling the interactions of microbes with their environment and with one another. While genomics can provide information regarding the genetic potential of microbes, proteomics characterizes the primary end-stage product, proteins, thus conveying functional information concerning microbial activity. Advances in mass spectrometry instrumentation and methodologies, along with bioinformatics approaches, have brought th... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=2823675 Wed, 23 Sep 2009 16:10:00 +0100 2823675 http://www.medworm.com/index.php?rid=2807803&cid=t_104194_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2009%2F09%2F17%2Fwikis-as-tools-in-genetics%2F I’ve been planning to write about these wikis that can be very useful tools in the hands of researchers for a long time. The first one is WikiPathway which is an open platform dedicated to the curation of biological pathways by and for the scientific community. The second is the WikiGenes which aims to build the database of evolutionary knowledge on Nature.com. The reason why I mention the third one now is there is a new publication focusing on the pros and cons of using a wiki in genetics research. In Wikipedia, Andrew and his friends created the Gene Portal a year ago and later analyzed the usability and the results. Annotating the function of all human genes is a critical, yet formidable, challenge. Current gene annotation efforts focus on centralized curation resources, but it ... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=2807803 Thu, 17 Sep 2009 20:38:24 +0100 2807803 http://www.medworm.com/index.php?rid=2766216&cid=t_104194_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2009%2F09%2F04%2Fwolframalpha-community-medicine-and-health%2F I use WolframAlpha because sometimes (if I know exactly what I want to find) it saves me plenty of time and clicks. If I want to calculate BMI, Google lists me several calculators. WolframAlpha calculates it itself. If I want to find information very fast about a clinical marker, Google gives me resources, WA gives me the best answer in one click. I also use it for ICD classification, as it’s more easily accessible than Wikipedia; for epidemiological data and other calculations. To sum it up, I think WolframAlpha is for those who perfectly know what they want to find and want to save time and clicks. For other search queries, Google is still the best. Now WolframAlpha launches communities and forums. Some medicine-related forums and interesting discussions: Health & Fitness: Lifesa... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=2766216 Fri, 04 Sep 2009 17:39:58 +0100 2766216 http://www.medworm.com/index.php?rid=2741537&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F08%2F28%2Ffriendfeed-life-scientists-14-day-summary%2F Since I haven’t posted for 14 days, what better (and lazier) way to post something than to surf over to a 14-day summary from the Life Scientists Group and link to the top ten items! Review process files in the EMBO Journal – but why only for “the majority of papers”? How XML threatens Big Data. Or not. How JSON might be an alternative – or not. Solve any computer problem – with this classic XKCD flowchart. Science reviews the revolution in ’strategic scientific reading’ – are they way behind the curve, or providing a useful summary for the uninitiated? Best practice in microbial genome annotation – spirited discussion on the nature of best bioinformatics practice. FriendFeed Life Scientists user survey – no further word on... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2741537 Fri, 28 Aug 2009 07:03:56 +0100 2741537 http://www.medworm.com/index.php?rid=2725172&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FOO7CVmfNFIc%2F Let’s see if it works. function initialize() { var wavePanel = new WavePanel("http://wave.google.com/a/wavesandbox.com/"); wavePanel.loadWave("wavesandbox.com!w+RqxqUECK%B"); wavePanel.init(document.getElementById('waveframe')); } (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=2725172 Fri, 21 Aug 2009 14:19:51 +0100 2725172 http://www.medworm.com/index.php?rid=2688839&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FKGuaEN4X-AU%2F (this will be a weekly post on the most important news of the week, things that caught our eyes here at Blind.Scientist headquarters) - Apparently there is a rich guy on the internet that likes to show off how many computers he has, but doesn’t know a lot about technology and stuff. Anyway, how not to write a post. Never used his website. - Skulpt is a nice project that I really like to see come to fruition. Check it out. - Universal health care, or whatever it will be, in US won’t be approved, because both parties are in the pocket of the (un)health industry. It’s like the joke where the father doctor leaves for vacation and leaves the clinic for his newly graduated son to take care. When he comes back, all his patients are cured, and the father says: “What the hel... Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=2688839 Mon, 10 Aug 2009 20:45:21 +0100 2688839 http://www.medworm.com/index.php?rid=2688840&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FKQ2Qbgl-mYU%2F The paper of this week touches a subject that I have been involved in the past: sequence simulation. INDELible, by Fletcher and Yang, is a program that is capable of simulating both DNA and amino acid sequences, and it seems to be the complete package to do so. It contains several substitution models and it can even simulate codon substitutions. As the article mentions, the closest comparison to INDELible is DAWG, developed by Reed Cartwright, that seems to be faster. DAWG is a nice program and generates good simulations and has a very well designed code with strong models and quite reliable results. And that’s what you want on a simulation program. You really want is a good implementation of the amino acid/nucleotide substitution pattern and a good model of indel simulation. It seem... Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=2688840 Mon, 10 Aug 2009 15:09:40 +0100 2688840 http://www.medworm.com/index.php?rid=2674437&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F08%2F06%2Frsruby-in-the-irb-console%2F R is terrific, of course, for all your statistical needs. But those data structures! “Everything is a list.” Leading to such wondrous ways to access variables as “p <- Meta(gds)$platform", or "last <- mylist[[1]][length(mylist[[1]])]". Sometimes, you want something more familiar. An array, a hash, a hash of arrays. Or, you may need to access R data in the language of your choice – e.g. as part of a Rails project. In Ruby, IRB is your friend. On the right, an IRB session in which we invoke RSRuby, load the GEOquery library from Bioconductor, fetch a dataset from the GEO database and examine the metadata that describes the experiment. Result: a ruby hash of arrays, where the keys are covariate types (”sample, disease.state, description&#8221... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2674437 Thu, 06 Aug 2009 06:36:52 +0100 2674437 http://www.medworm.com/index.php?rid=2664078&cid=t_104194_132_f&fid=35021&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FYourBonesGotALittleMachine%2F%7E3%2F0uYcK8L_BL4%2F Discussion” tab, ala Wikipedia (not pictured). • Each field, or block of related fields, would have an Add/edit button at the top right of the block. (I’ve chosen the Universal Edit Button as an example) Aftertought: Maybe putting these features under tabs isn’t quite the best place, since the existing tabs are ‘actions’ that can be taken rather than ‘extra info’ to be viewed. This UI detail could certainly be refined. This proposal has many wiki-like features (history, attribution, open editing, curation by trusted users and potentially page/section locking) but doesn’t really fit my definition of a wiki since the input format is not free-form wiki-text, but is instead constrained by the interface to enforce the submission of (mostly) st... Your bones got a little machine. blogs http://www.medworm.com/rss/comments.php?id=2664078 Mon, 03 Aug 2009 09:21:56 +0100 2664078 http://www.medworm.com/index.php?rid=2653944&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F07%2F30%2Fhow-to-combinations-of-covariates-using-ruby%2F I work with people who generate a lot of microarray data. One question that they often ask is: can we find those genes with a two-fold or more change in median expression under two or more different conditions? For example, let’s say that we have 3 conditions: “normal”, “adenoma” and “cancer”. That gives us 3 pairwise comparisons: normal-adenoma, normal-cancer and adenoma-cancer. Here’s a Ruby solution to the problem. First, I installed StatArray, a Ruby gem that provides statistical methods for array objects. It’s not been updated for 3 years, but seems to work. require 'rubygems' require 'statarray' Next, credit to David Burger for posting this code solution for combinations in Ruby. You give it an array of ele... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2653944 Thu, 30 Jul 2009 07:08:38 +0100 2653944 http://www.medworm.com/index.php?rid=2634592&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F07%2F24%2Frsruby-and-rails-revisited%2F A couple of months ago, I wrote a brief guide to displaying R plots in a Rails application using RSRuby. It worked at the time – really it did – but since then, I’ve encountered problems. One is that despite sending the plot output to a PNG file, R X11 windows started to pop up on loading the web page containing the plot. Another is the appearance of long error messages related to “stack smashing” on terminating Mongrel server. Fortunately, I read an excellent guide by Ana Nelson, R on Rails with RSRuby, which convinced me that I was doing things all wrong. So here is an amended version of my R + RSRuby + Rails “Hello World” application. We start as usual with “rails Plotter”. Next, I like to delete the public/index.html file and gener... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2634592 Fri, 24 Jul 2009 01:15:57 +0100 2634592 http://www.medworm.com/index.php?rid=2598422&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2Frapo97qwDT8%2F I usually don’t get personal with software reviews. I even praised TNT in the past for being extremely fast, even though it mainly does maximum parsimony. But Mendeley’s case is outstanding and their attempt to censor me, makes things personal. I’m the closest you can get to be a “no one” in the scientific realm, I have this blog, a site needing updates and a couple of applications that no one uses. I still have a voice, maybe a smallish one, but I have. And I don’t like hype. And I’m a masochist. So, after reading several hype-like entries on the internet about how hyper-super-duper is the new Mendeley’s version, I decided to go against the attempted censorship (I guess everyone at Mendeley Corp, or Inc, vote for BNP) and common sense, and d... Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=2598422 Mon, 13 Jul 2009 17:07:36 +0100 2598422 http://www.medworm.com/index.php?rid=4098289&cid=t_104194_132_f&fid=35016&url=http%3A%2F%2Ffgibson.com%2F2009%2F07%2F10%2Fattribution-vs-citation-do-you-know-the-difference%2F This article outlines the differences between attribution and citation, and suggests that what most scientists are interested in is not attribution, which can be ensured via licensing restrictions, but instead citation, which is a much tougher nut to crack. At ISMB last week, there were a number of conversations about the difference between attribution and citation. This topic was brought up again yesterday in a conversation between the two authors of this post, Frank and Allyson. It is an important distinction which is explored in this post. First, some definitions for attribution and citation. These are not the only definitions possible, but for the purposes of this discussion, please keep these in mind. Attribution: Acknowledgement of the use of someone else’s information, data, ... peanutbutter blogs http://www.medworm.com/rss/comments.php?id=4098289 Fri, 10 Jul 2009 12:23:45 +0100 4098289 http://www.medworm.com/index.php?rid=2571048&cid=t_104194_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F07%2F03%2Fgreat-work-ismb-microblogging-team%2F Another year, another ISMB/ECCB meeting and – another great blogging effort. It’s all at the FriendFeed group: ISMB/ECCB Stockholm 2009, with outgoing links to individual blogs too. Thanks and congratulations to all involved for a great effort. Looking forward to the official write-up. Posted in bioinformatics, computing, meetings, web resources Tagged: friendfeed, iscb, ismb, microblogging (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2571048 Fri, 03 Jul 2009 00:42:35 +0100 2571048 http://www.medworm.com/index.php?rid=2510951&cid=t_104194_107_f&fid=35041&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fscienceblogs%2Fdigitalbio%2F%7E3%2FGLG5iAMbykM%2Feducating_students_for_a_caree.php For those of you who may have been wondering where I've been, these past few weeks have seen me grading final projects, writing a chapter on analyzing Next Gen DNA sequencing data for the Current Protocols series, and flying back and forth between Seattle and various meetings elsewhere in the U.S. It will probably take years of bike commuting to make up for my carbon credits, but most meetings I attend don't have viable alternatives in venues like Second Life or World of Warcraft. Anyway, as I sit writing on an airplane, I think I could revise the title for Dr. Seuss' famous book to "Oh the places I've been." Inside the tropical house at the Missouri Botanical Garden Read the rest of this post... | Read the comments on this post... (Source: Discovering Biology in a Digital World) Discovering Biology in a Digital World blogs http://www.medworm.com/rss/comments.php?id=2510951 Sat, 20 Jun 2009 18:01:38 +0100 2510951 http://www.medworm.com/index.php?rid=2474070&cid=t_104194_136_f&fid=37846&url=http%3A%2F%2Fhealthinfoispower.wordpress.com%2F2009%2F06%2F10%2Fone-in-three-billion-found-single-mutation-in-the-foxl2-gene-may-cause-granulosa-cell-ovarian-cancer%2F “… Vancouver scientists from the Ovarian Cancer Research (OvCaRe) Program at BC Cancer Agency and Vancouver Coastal Health Research Institute have discovered that there appears to be a single spelling mistake in the genetic code of granulosa cell tumours, a rare and often untreatable form of ovarian cancer. This means that out of the three [...] (Source: Libby's H*O*P*E*) Libby's H*O*P*E* blogs http://www.medworm.com/rss/comments.php?id=2474070 Thu, 11 Jun 2009 06:05:16 +0100 2474070 http://www.medworm.com/index.php?rid=4098290&cid=t_104194_132_f&fid=35016&url=http%3A%2F%2Ffgibson.com%2F2009%2F06%2F07%2Fthe-obo-foundry-principles%2F This week, is a week long ontology building week, consisting of two days at the OBO Foundry workshop followed by 4 days at the OBI workshop, all hosted at the EBI. In advance of the meeting (even though I am writing this during the meeting) Duncan asked “how can the ontology development principles be improved“. Ally and Melanie responded commenting on each principle, and I would pretty much agree with every issue the ontology ladies raise. These principles should be used to guide ontology developers to build a consistent resource and which are used to “peer-review” the ontology. However, my concern is that there is no indication or recommended methodology in how these principles could be met, during the development process. This was my motivation for reviewing all t... peanutbutter blogs http://www.medworm.com/rss/comments.php?id=4098290 Sun, 07 Jun 2009 10:01:17 +0100 4098290 http://www.medworm.com/index.php?rid=2452990&cid=t_104194_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FRcRUMytM4n4%2F Yes, you do. I know because you’re hip, right? No. Do you want to publish a paper about it? Yes. But that’s so 2008. Shouldn’t you wait for Google Wave? Maybe. Now, seriously. There’s a current discussion on the subject after CSHL threatened to forbid anyone to liveblog/tweet/friendfeed presentations at their conferences if they don’t follow the usual rules for media coverage. That’s outrageous! No, it’s not. That’s what they want to do, let them do it. They have the right to forbid anyone to broadcast whatever is going on during presentations at the conferences they organize. They are organizing it, they are paying for it (relatively speaking) and they spent time organizing it. Whenever you registered, if there are rules specifying what you ... Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=2452990 Wed, 03 Jun 2009 23:42:54 +0100 2452990